Non-European Union citizens entering Portugal through an EU border without passport control may need to hand in a "Declaration of Entry" at the nearest Portuguese Foreign Office. To do that, citizens have to schedule an appointment within three working days after arrival. Please check this page to see if you need to hand in such a declaration. Failing to do this implies the payment of a fine.
This registration applies to European Union, European Economic Area, Andorra and Switzerland citizens, staying for more than 3 months, and has to be done at the City Hall (“Câmara Municipal”) desk at Loja do Cidadão.