France, Portugal, Germany and Spain on Tuesday struck a deal to take in migrants from the Mediterranean rescue ship Aquarius, after they are brought to Malta, ending another migrant saga at sea.

Portugal said it had agreed to take 10 of the 58 migrants on board as part of a "response of solidarity to the flow of migrants seeking to reach Europe across the Mediterranean".

It was not immediately clear how many migrants France, Germany and Spain had agreed to take in or where the ship would dock.

In a statement, the Maltese government said Malta and France took "a joint initiative" to solve the current impasse with regard to the situation of MV Aquarius.

The 58 persons on board MV Aquarius will be disembarked on a Maltese boat in international waters before they are redistributed to the other countries. 

"The operation will take place as soon as it is logistically possible," the government said. 

"The government of Malta is participating in this effort on purely humanitarian grounds and without prejudice to its position on search and rescue activities, which remain unchanged."

Considering the fact that the MV Aquarius has been deflagged, the vessel will proceed to its home port to rectify its stateless position, the government said.

"The governments of France and Malta remain committed to a multilateral and proactive approach based on the rule of law and solidarity."

Earlier on Tuesday, France said it was not ready to let the Aquarius dock in Marseille, as suggested by the charities operating the ship, adding that a European solution involving the nearest port, Malta, was in the works.

On Sunday, Italian Interior Minister Matteo Salvini of the far-right League Party said the Aquarius had hindered the work of the Libyan coast guard and Italy's ports would remain shut.

Vessel is only NGO vessel operating in central Mediterranean

In August, France and Malta struck a deal to let the Aquarius dock in Valletta harbour after France, Germany, Luxembourg, Portugal and Spain agreed to take in the migrants, ending a five-day tug-of-war among EU countries.

Aquarius 2 is the one remaining charity rescue vessel still operating in the central Mediterranean, picking up migrants who are in most cases trying to get to Europe from Libya, often in overcrowded, unseaworthy boats.

On Monday, Panama authorities revoked the Aquarius's registration, meaning that once it docks it will be 'de-flagged' and will not have the right to sail unless a new registration is found.

A public backlash over the arrival of hundreds of thousands of migrants in the past five years has fuelled a swing towards far-right parties in many countries in Europe and helped bring Italy's anti-establishment ruling coalition to power earlier this year.