A group of 265 migrants were brought to Malta on Saturday, including 36 from the rescue ship Ocean Viking, but the operators of the ship complained that more than 180 other migrants on board had been refused disembarkation by the island.
The Maltese armed forces said 229 migrants among Saturday's arrivals were rescued from three boats in distress in Malta's search and rescue zone.
Another 36 were transferred to a Maltese patrol boat from the Ocean Viking, which had rescued them in Malta's zone.
The arrivals were the fourth group to arrive on the Mediterranean island in a week.
But Medecins Sans Frontieres (MSF), which operates Ocean Viking, said in a tweet that 182 survivors from other rescues, including a newborn, children and a pregnant woman, remained stranded on board.
This, it said, "demonstrates the discriminatory, arbitrary and inhumane nature of a system which continues to prioritise political gameplay above human lives and dignity".
Malta argued that those people were picked up outside its rescue zone.
The island took more than 300 migrants from the Ocean Viking in August on condition that they would be shared among other EU countries, but most are still on the island, stretching its limited reception facilities.
The plight of the Ocean Viking, run by MSF and another French charity, SOS Méditerranée, has exposed Europe's failure to come up with a coherent policy to deal with migration from Africa through Libya.
EU states have been at loggerheads over how to handle refugees and migrants reaching its shores since a 2015 spike in Mediterranean arrivals of people fleeing conflicts and poverty in the Middle East and Africa.
On Monday Malta will host an EU home affairs ministers meeting which will discuss migration and how EU states may share arrivals.