Over the past several years, the United States has embarked on a program of secret research on biological weapons that, some officials say, tests the limits of the global treaty banning such weapons.

The 1972 treaty forbids nations from developing or acquiring weapons that spread disease, but it allows work on vaccines and other protective measures. Government officials said the secret research, which mimicked the major steps a state or terrorist would take to create a biological arsenal, was aimed at better understanding the threat.

The projects, which have not been previously disclosed, were begun under President Clinton and have been embraced by the Bush administration, which intends to expand them.

Earlier this year, administration officials said, the Pentagon drew up plans to engineer genetically a potentially more potent variant of the bacterium that causes anthrax, a deadly disease ideal for germ warfare.

The experiment has been devised to assess whether the vaccine now being given to millions of American soldiers is effective against such a superbug, which was first created by Russian scientists. A Bush administration official said the National Security Council is expected to give the final go-ahead later this month.

Two other projects completed during the Clinton administration focused on the mechanics of making germ weapons.

In a program code-named [Project Clear Vision], the Central Intelligence Agency built and tested a model of a Soviet-designed germ bomb that agency officials feared was being sold on the international market. The C.I.A. device lacked a fuse and other parts that would make it a working bomb, intelligence officials said.

At about the same time, Pentagon experts assembled a germ factory in the Nevada desert from commercially available materials. Pentagon officials said the project demonstrated the ease with which a terrorist or rogue nation could build a plant that could produce pounds of the deadly germs.

Both the mock bomb and the factory were tested with simulants -- benign substances with characteristics similar to the germs used in weapons, officials said.

A senior Bush administration official said all the projects were ''fully consistent'' with the treaty banning biological weapons and were needed to protect Americans against a growing danger. ''This administration will pursue defenses against the full spectrum of biological threats,'' the official said.

The treaty, another administration official said, allows the United States to conduct research on both microbes and germ munitions for ''protective or defensive purposes.''

Some Clinton administration officials worried, however, that the project violated the pact. And others expressed concern that the experiments, if disclosed, might be misunderstood as a clandestine effort to resume work on a class of weapons that President Nixon had relinquished in 1969.

Simultaneous experiments involving a model of a germ bomb, a factory to make biological agents and the developoment of more potent anthrax, these officials said, would draw vociferous protests from Washington if conducted by a country the United States viewed as suspect.

Administration officials said the need to keep such projects secret was a significant reason behind President Bush's recent rejection of a draft agreement to strengthen the germ-weapons treaty, which has been signed by 143 nations.

The draft would require those countries to disclose where they are conducting defensive research involving gene-splicing or germs likely to be used in weapons. The sites would then be subject to international inspections.

Many national security officials in both the Clinton and Bush administrations opposed the draft, arguing that it would give potential adversaries a road map to what the United States considers its most serious vulnerabilities.

Among the facilities likely to be open to inspection under the draft agreement would be the West Jefferson, Ohio, laboratory of the Battelle Memorial Institute, a military contractor that has been selected to create the genetically altered anthrax.

Several officials who served in senior posts in the Clinton administration acknowledged that the secretive efforts were so poorly coordinated that even the White House was unaware of their full scope.

The Pentagon's project to build a germ factory was not reported to the White House, they said. President Clinton, who developed an intense interest in germ weapons, was never briefed on the programs under way or contemplated, the officials said.

A former senior official in the Clinton White House conceded that in retrospect, someone should have been responsible for reviewing the projects to ensure that they were not only effective in defending the United States, but consistent with the nation's arms-control pledges.

The C.I.A.'s tests on the bomb model touched off a dispute among government experts after the tests were concluded in 2000, with some officials arguing that they violated the germ treaty's prohibition against developing weapons.

Intelligence officials said lawyers at the agency and the White House concluded that the work was defensive, and therefore allowed. But even officials who supported the effort acknowledged that it brought the United States closer to what was forbidden.

''It was pressing how far you go before you do something illegal or immoral,'' recalled one senior official who was briefed on the program.

Public disclosure of the research is likely to complicate the position of the United States, which has long been in the forefront of efforts to enforce the ban on germ weapons.

The Bush administration's willingness to abandon the 1972 Antiballistic Missile treaty has already drawn criticism around the world. And the administration's stance on the draft agreement for the germ treaty has put Washington at odds with many of its allies, including Japan and Britain.

The Original Treaty

During the cold war, both the United States and the Soviet Union produced vast quantities of germ weapons, enough to kill everyone on earth.

Eager to halt the spread of what many called the poor man's atom bomb, the United States unilaterally gave up germ arms and helped lead the global campaign to abolish them. By 1975, most of the world's nations had signed the convention.

In doing so, they agreed not to develop, produce, acquire or stockpile quantities or types of germs that had no ''prophylactic, protective or other peaceful purposes.'' They also pledged not to develop or obtain weapons or other equipment ''designed to use such agents or toxins for hostile purposes or in armed conflict.''

There were at least two significant loopholes: The pact did not define ''defensive'' research or say what studies might be prohibited, if any. And it provided no means of catching cheaters.

In the following decades, several countries did cheat, some on a huge scale. The Soviet Union built entire cities devoted to developing germ weapons, employing tens of thousands of people and turning anthrax, smallpox and bubonic plague into weapons of war. In the late 1980's, Iraq began a crash program to produce its own germ arsenal.

Both countries insisted that their programs were for defensive purposes.

American intelligence officials had suspected that Baghdad and Moscow were clandestinely producing germ weapons. But the full picture of their efforts did not become clear until the 1990's, after several Iraqi and Soviet officials defected.

Fears about the spread of biological weapons were deepened by the rise of terrorism against Americans, the great strides in genetic engineering and the collapse of the Soviet Union, which left thousands of scientists skilled in biological warfare unemployed, penniless and vulnerable to recruitment.

The threat disclosed a quandary: While the United States spent billions of dollars a year to assess enemy military forces and to defend against bullets, tanks, bombs and jet fighters, it knew relatively little about the working of exotic arms it had relinquished long ago.

Designing a Delivery System

In the mid-1990's, the C.I.A. and other intelligence agencies stepped up their search for information about other nations' biological research programs, focusing on the former Soviet Union, Iran, Iraq and Libya, among others. Much of the initial emphasis was on the germs that enemies might use in an attack, officials said.

But in 1997, the agency embarked on Clear Vision, which focused on weapons systems that would deliver the germs.

Intelligence officials said the project was led by Gene Johnson, a senior C.I.A. scientist who had long worked with some of the world's deadliest viruses. Dr. Johnson was eager to understand the damage that Soviet miniature bombs -- bomblets, in military parlance -- might inflict.

The agency asked its spies to find or buy a Soviet bomblet, which releases germs in a fine mist. That search proved unsuccessful, and the agency approved a proposal to build a replica and study how well it could disperse its lethal cargo.

The agency's lawyers concluded that such a project was permitted by the treaty because the intent was defensive. Intelligence officials said the C.I.A. had reports that at least one nation was trying to buy the Soviet-made bomblets.

A model was constructed and the agency conducted two sets of tests at Battelle, the military contractor. The experiments measured dissemination characteristics and how the model performed under different atmospheric conditions, intelligence officials said. They emphasized that the device was a ''portion'' of a bomb that could not have been used as a weapon.

The experiments caused concern at the White House, which learned about the project after it was under way. Some aides to President Clinton worried that the benefits did not justify the risks. But a White House lawyer led a joint assessment by several departments that concluded that the program did not violate the treaty, and it went ahead.

The questions were debated anew after the project was completed, this time without consensus. A State Department official argued for a strict reading of the treaty: the ban on acquiring or developing ''weapons'' barred states from building even a partial model of a germ bomb, no matter what the rationale.

''A bomb is a bomb is a bomb,'' another official said at the time.

The C.I.A. continued to insist that it had the legal authority to conduct such tests and, intelligence officials said, the agency was prepared to reopen the fight over how to interpret the treaty. But even so, the agency ended the Clear Vision project in the last year of the Clinton administration, intelligence officials said.

Bill Harlow, the C.I.A. spokesman, acknowledged that the agency had conducted ''laboratory or experimental'' work to assess the intelligence it had gathered about biological warfare.

''Everything we have done in this respect was entirely appropriate, necessary, consistent with U.S. treaty obligations and was briefed to the National Security Council staff and appropriate Congressional oversight committees,'' Mr. Harlow said.

Breeding More Potent Anthrax

In the 1990's, government officials also grew increasingly worried about the possibility that scientists could use the widely available techniques of gene-splicing to create even more deadly weapons.

Those concerns deepened in 1995, when Russian scientists disclosed at a scientific conference in Britain that they had implanted genes from Bacillus cereus, an organism that causes food poisoning, into the anthrax microbe.

The scientists said later that the experiments were peaceful; the two microbes can be found side-by-side in nature and, the Russians said, they wanted to see what happened if they cross-bred.

A published account of the experiment, which appeared in a scientific journal in late 1997, alarmed the Pentagon, which had just decided to require that American soldiers be vaccinated against anthrax. According to the article, the new strain was resistant to Russia's anthrax vaccine, at least in hamsters.

American officials tried to obtain a sample from Russia through a scientific exchange program to see whether the Russians had really created such a hybrid. The Americans also wanted to test whether the microbe could defeat the American vaccine, which is different from that used by Russia.

Despite repeated promises, the bacteria were never provided.

Eventually the C.I.A. drew up plans to replicate the strain, but intelligence officials said the agency hesitated because there was no specific report that an adversary was attempting to turn the superbug into a weapon.

This year, officials said, the project was taken over by the Pentagon's intelligence arm, the Defense Intelligence Agency. Pentagon lawyers reviewed the proposal and said it complied with the treaty. Officials said the research would be part of [Project Jefferson], yet another government effort to track the dangers posed by germ weapons.

A spokesman for Defense Intelligence, Lt. Cmdr. James Brooks, declined comment. Asked about the precautions at Battelle, which is to create the enhanced anthrax, Commander Brooks said security was ''entirely suitable for all work already conducted and planned for Project Jefferson.''

The Question of Secrecy

While several officials in both the Clinton and Bush administrations called this and other research long overdue, they expressed concern about the lack of a central system for vetting such proposals.

And a former American diplomat questioned the wisdom of keeping them secret.

James F. Leonard, head of the delegation that negotiated the germ treaty, said research on microbes or munitions could be justified, depending on the specifics.

But he said such experiments should be done openly, exposed to the scrutiny of scientists and the public. Public disclosure, he said, is important evidence that the United States is proceeding with a ''clean heart.''

''It's very important to be open,'' he said. ''If we're not open, who's going to be open?''

Mr. Leonard said the fine distinctions drawn by government lawyers were frequently ignored when a secret program was exposed. Then, he said, others offer the harshest possible interpretations -- a ''vulgarization of what has been done.''

But he concluded that the secret germ research, as described to him, was ''foolish, but not illegal.''

The authors have reported on biological weapons for The New York Times and based this article on material gathered for their book, ''Germs: Biological Weapons and America's Secret War,'' which is being published this month by Simon & Schuster Inc.