At least 44 Bangladeshi nationals who are among the migrants rescued from the Mediterranean will be sent back home, The Telegraph newspaper reported on Wednesday.
However, the conditions of the Bangladeshi migrants could not be verified by any other source.
Almost 300 migrants rescued when they were trying to reach Europe from North Africa in recent times, are reportedly in Malta.
The British newspaper quoting prime minister Joseph Muscat said that 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.
"An ad hoc agreement has been reached," he was quoted to have told journalists, adding that it also included a decision on the fate of 249 rescued migrants already in Malta.
Of the total of 298 migrants, 176 would be sent to Germany, France, Portugal, Ireland, Romania, Luxembourg, the Netherlands and Italy, said the Telegraph report.
Another 78 will be allowed to stay in Malta.
A total of 44 Bangladeshi migrants will be sent back to their country, the report added.
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, the report mentioned.
They, it pointed out, 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, the report said.
"Malta never closed its ports and it is still a safe port," the prime minister was quoted to have said. He previously complained reportedly that his country has to bear an unfair share of migrant numbers.