Italy agreed to take on 78 migrants who refused to be brought to Malta after being rescued last night.
The protests of the migrants, who are in reportedly good health, triggered off discussions between the two countries.
Another five migrants accepted to be brought to Malta and arrived in a patrol boat during the night.
The Armed Forces of Malta said the migrants were rescued off the east coast of Malta from a boat by the Panama-registered merchant vessel Tychy.
The boat, which was in international waters but within Malta's search and rescue region, had been taking in water.
Malta, which had been at the forefront of boat migrant crisis for years, has received just 100 asylum seekers in 2015. Thousands of migrants rescued off Libya have instead been transported to Italy.