The forty migrants were transferred to the Armed Force of Mala (AFM) vessel outside Maltese territorial waters on Sunday morning, and disembarked at AFM naval base in Floriana at around 11 a.m. local time.
The asylum seekers are mainly West African and are claiming to be from Cameroon, Ivory Coast, Ghana, Liberia, Togo and Mali.
Maltese Prime Minister Joseph Muscat announced on Saturday that the migrants will be allowed to disembark following a request from Germany.
None of the migrants will remain in Malta and will be relocated to other EU member states.
Earlier in the week, Italian authorities denied the rescue ship permission to enter the port.
The migrants have been at sea since Wednesday night, when the rescue boat Alan Kurdi operated by Sea-Eye rescued them at sea off the coast of Libya.
