This announcement was made shortly after it emerged on Tuesday that Porto had lost out on accommodating the European Medicines Agency, which is to leave the UK following Brexit, to Amsterdam.
Some reports have suggested the decision was made to move Infarmed from Lisbon to Porto to go some way towards making up for the loss of the European agency, although this was rubbished by Porto Mayor, Rui Pereira.
Infarmed, which regulates and supervises medicines, medical devices and cosmetic products in Portugal, will operate from Porto from January 2019 and keep Lisbon as a regional nucleus.
Meanwhile, news that Infarmed will be moving to Porto has been poorly received by its circa-350 workers.
The head of the watchdog said he only learned of the decision hours before an official statement was made by the Health Minister.
Employees have this week held a plenary in which they discussed their concerns, and the fact they were left in the dark.