"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.
The Prime Minister said that how the situation was handled was "a matter of principle" so not to set a precedent and turn Malta into a centre where boats carrying rescued migrants from any part of the Mediterranean could go.
"That is why we are stressing that we do not want this case to set a precedent".
Muscat said that Malta's own naval vessels had in recent days rescued 250 migrants, with the government saying some of them were pulled to safety closer to Italian waters.
Some migrants arrive at Malaga's port after been rescued by Spanish Salvamento Maritimo, in Malaga, Andalusia, Spain, 06 January 2018.
He underlined that Malta had no obligation to take the migrants in, and that, in this case, other European Union countries had also refused to accept them. He also questioned whether Malta would be getting any help from other countries in dealing with the 249 migrants that they had just rescued.
"I won't enter the controversies about the dynamics of this rescue but I think it's a known fact", he said.
Muscat said that Malta's position when it came to dealing with migration was "very simple" and was based on namely two principles which go hand-in-hand: firstly that human life is safeguarded and secondly that there are no compromises on national security. Two NGO ships are in Maltese territorial water: "the people on board should be made to disembark in Valletta", he said.
Pope Francis has appealed to European leaders to show "concrete solidarity" and allow 49 migrants aboard two ships in the Mediterranean to land.
Pope Francis brought the issue to worldwide attention on Sunday, when he urged European leaders to show "concrete solidarity regarding these people".