He has appealed to EU member states to take some of the more than 200 detainees at the camp - some of whom cannot go back to their home countries for fear of reprisals.
The Portuguese ministry has not identified the detainees and has not given any indication as to when they will arrive in Portugal.
In its statement, the foreign ministry heralded the planned closure of the US prison in Cuba as "a milestone for the renewal of transatlantic relations and a victory for those who defend and encourage respect for human rights within the context of the fight against terrorism".
The other nations in the EU to accept individuals held at Gauntanamo after Ireland and France.
Outside the 27-member bloc, a few former detainees have been accepted in Albania and Bermuda.
Britain has said it will only accept former Guantanamo prisoners who have citizenship or residency links, while Germany and Sweden say they want more of a compelling reason from the US as to why they should accept former inmates of the prison.
In June, the EU said it was up to individual EU members to decide whether to accept former Guantanamo prisoners.
Silvio Berlusconi, Italy's prime minister, recently told Obama that his country would take three detainees, but details of a deal have been kept secret.
Spain is assessing a US appeal to take four detainees held at the prison.