Archbishop Charles Scicluna visited the Auberge de Castille on Thursday and had talks with Prime Minister Robert Abela.
The prime minister disclosed the meeting in a tweet.
Mgr Scicluna was accompanied by the auxiliary bishop Joseph Galea Curmi.
The bishops met a number of employees and were also introduced to Mrs Abela.
Soon after being sworn-in Abela had made a courtesy call on the archbishop.
Mgr Scicluna over the past days has been critical of the government's decision to close Malta's harbours for migrants. The Maltese episcopal conference also wrote to the Vatican, urging it to intervene so that migrants could be brought to Malta and then shared by other countries.