Malta's prime minister on Sunday promised a major clean-up operation after devastating gale-force winds caused major damage and disruption on the Mediterranean island.

Some 117 migrants who left Libya in a rubber dinghy two days ago are unaccounted for, the International Organisation for Migration (IOM) said on Saturday, after three people were rescued from the vessel after it sank in the Mediterranean.

France is not ready for now to allow the Mediterranean rescue ship Aquarius to dock and disembark dozens of migrants at the port of Marseille, France's finance minister said on Tuesday.

The Aquarius rescue ship arrived in Malta on Wednesday after EU countries thrashed out a deal to take in the 141 migrants onboard, defusing another diplomatic standoff in the Mediterranean.

Migrant rescue charities operating in the Mediterranean said Tuesday that an Italian boat may have violated international law by taking more than 100 migrants it had saved back to Libya.

A Spanish NGO said Saturday it had rescued 59 migrants as they tried to cross the Mediterranean from Libya, drawing condemnation from Italy's far-right interior minister who said they were not welcome in his country.

The lifeless bodies of three babies were brought ashore in Libya on Friday, victims of a Mediterranean migrant shipwreck in which survivors say 100 people are still missing.

Libya's coastguard has rescued nearly 1,000 migrants who were on boats in distress in the Mediterranean on their way to Europe, the navy said on Monday.

The International Commission on Missing Persons (ICMP) launched an initiative in Rome on Monday to help find missing migrants in the Mediterranean, a day after Italy and Malta refused to allow a rescue boat carrying 629 migrants to dock in their ports.

The migrants, including pregnant women and scores of children, were saved by the French charity SOS Mediterranee on Saturday.

Tunisian authorities said 47 bodies were recovered off the country's southern coast, close to the city of Sfax, while 68 people were rescued.

German rescuers said on Saturday they had saved 128 migrants from an overcrowded boat floating in the Mediterranean after it lost the ability to steer.