Malta has reached a deal with other EU member states to allow 49 migrants aboard two rescue ships off the coast of the island nation to disembark, Prime Minister Joseph Muscat said on Wednesday.

"An ad hoc agreement has been reached," Muscat told journalists, adding that it also included a decision on the fate of 249 rescued migrants already in Malta.

The 49 migrants, including a baby and several children, were rescued while attempting the dangerous Mediterranean crossing from North Africa to Europe.

Muscat said that of the total of 298 migrants, 176 would be sent to Germany, France, Portugal, Ireland, Romania, Luxembourg, the Netherlands and Italy.

Another 78 will be allowed to stay in Malta, and 44 Bangladeshi migrants will be sent back to their country.

The migrants have been stranded off the coast of Malta on the Sea-Watch and another boat since late last year, with no country allowing them to dock, suffering sea sickness and dehydration, with some briefly refusing food.

They have been unable to disembark because of a diplomatic deadlock among EU member states, despite an appeal by Pope Francis on Sunday for EU leaders to show solidarity.

On Tuesday Malta appeared to raise the stakes still further, saying that any deal on the fate of the 49 must include that of the 249 rescued migrants already on the island.

"Malta never closed its ports and it is still a safe port," said Muscat, who has previously complained that his country has to bear an unfair share of migrant numbers.

"We wanted to send a strong political message that the burden must be shared because it is a European issue... Every hour that passed without a solution was not an hour I was proud of," he said.