Malta on Monday refused permission for an Italian navy ship carrying rescued migrants to dock in Valletta.
Italian authorities then instructed the ship carrying 69 African migrants, including 16 women, to head for Porto Empedocle in Sicily.
Italian authorities said the rescue took place in waters where Malta has responsibility for search and rescue operations.
But they said the eventual decision to take the migrants to Sicily was taken in agreement with Maltese authorities which coordinated the operation.
Earlier this month the two countries were engaged in a four-day stand-off over migrants picked up in disputed waters, who were eventually taken to Italy.
Partly to resolve such disputes, Italy with Malta's backing last week started taking migrants rescued in international waters straight back to Libya to be processed.
Humanitarian organisations and the Catholic Church have raised concerns for asylum seekers but the Italian and Malta governments have underscored the importance of discouraging migrants from putting themselves in the hands of traffickers.
