New Interior Minister of Italy, Matteo Salvini, have denied permission for a rescue ship conveying about 629 migrants to dock, thereby leaving them stranded.
The migrants, who are mostly children, were picked up in six different rescue operations off Libya's coast, BBC reports.
The leader of the right-wing League party, had promised during Italy's recent general election to take tougher measures concerning migration.
He says Malta should accept the Aquarius, but it refused, arguing that it falls under Italy's jurisdiction.
Italy is the major entry point for migrants crossing from North Africa to Europe.
German charity SOS Méditerranée says the Italian Maritime Rescue Co-ordination Centre has instructed the ship to stand by in its current position, 35 nautical miles (65km) from Italy and 27 nautical miles from Malta.
Mr Salvini says another ship has rescued hundreds more migrants near Libya and is heading for Italy.
"Italy has stopped bowing its heads to obey, this time there are those who say NO," he tweeted.
"Most of them are sleeping outside. They are obviously exhausted, they have been exposed to the elements, they have been at sea for 20 to 30 hours prior to their rescue," she told the BBC.
"They are fragile and we have yet to learn what's going to happen to them," she added.