"We have indicated we are ready to welcome around 10 people: that is women and children and both Malta and Sea Watch are creating obstructions, by not allowing them to disembark and keeping them aboard", he told Italian daily, Corriere della Sera.
Malta is also refusing to let the boats dock or the migrants disembark, but has allowed the two boats to enter its waters for fresh supplies.
This is not the first time the Argentinian pope, himself descended from Italian immigrants, has appealed to European leaders to open their borders. "That's the line and it will not change".
Joseph Muscat said on Sunday, during a One Radio interview, that it was his responsibility to avoid setting a precedent by accepting to take in the 49 migrants who are now stranded off Malta's coast on two NGO ships. ".We are discussing with other countries and the European Union to tell us whose responsibility this case was, and if a similar situation arises, who takes responsibility".
"This is an issue that might set a precedent and we should be vigilant about it", he told Malta's Radio One station.
If Malta let in migrants from the two rescue ships, "the bullies would have won", he added.
The small island state of Malta, which has a population of just 450,000, sits in the middle of the Mediterranean, not far from the Libyan coast.
The Pope has appealed to European leaders to provide refuge for 49 migrants trapped on two rescue ships and buffeted by winter storms off Malta for more than two weeks.
Charities and United Nations agencies have called on European leaders to take in the vessels as they wait in the Mediterranean.
49 people are now stranded in Maltese waters on two NGO-run vessels, the Sea-Watch 3 and the Sea-Eye.
Spain's maritime rescue service says it has saved 549 migrants trying to cross the Mediterranean Sea. Among them are a one-year-old baby and two children aged six and seven.