Unfortunately different sources of Portuguese data use different names and/or codes for the different regions of Portugal.
Here are some files that you may find useful in case you are working with data from different sources.
INE NUTS 2001 - this file contains the order presented in INE series including NUTS I, II, III (according to 2001 code), and municipalities
INE NUTS 2013 - this file contains the order presented in INE series including NUTS I, II, III (according to 2013 code), and municipalities
Pordata - this file contains the order presented in Pordata series including NUTS I, II, III (according to 2013 code, including some extra for the islands), and municipalities
If you are using Marktest or Quadros de Pessoal both datasets use the variable "code" that is included in all 3 files above.
In case you merge the data with other sources that do not have a code for the regions, you might find this Stata program useful: removeacc substitutes all the letters with accents (e.g. Ă ) with the respective letter without accent. Useful as well might be to import the data using the Western language option so that the accents are not converted into unknown characters.