The Aquarius, chartered by French aid group SOS Mediterranee, was due to leave the southern port of Marseille later Wednesday nearly two months after Italy and Malta refused to let it dock with 630 migrants onboard, sparking a bitter international row who would take them in.

“Nothing except a threat to the security of our ship… will make us give up our triple mission: saving, protecting, bearing witness,” the NGO's chief Francis Vallat told a press conference.

The ship has been docked for a month for maintenance work following the row, which saw Italy's populist government insist it had had enough of NGOs dropping rescued migrants on its shores.

After being stranded at sea for days, the migrants onboard the Aquarius were eventually allowed to dock in Spain.

The crisis prompted EU leaders to seek a compromise deal at a summit meeting in late June, which could lead to “disembarkation platforms” outside 
the bloc, most likely in north Africa, to discourage migrants boarding EU-bound smuggler boats.

SOS Mediterranee says it has a humanitarian duty to prevent  migrants — mostly sub-Saharan Africans — from drowning as they attempt the perilous Mediterranean crossing in rickety boats.

The group has picked up nearly 30,000 people since it launched its rescue operations in February 2016. Over the past four years, at least 15,000 people have drowned trying to make the journey, it said in a statement.

While docked, the ship has re-stocked with food and improved its sanitary facilities, including better waste treatment to prevent diseases spreading onboard.

In recent weeks Spain has overtaken Italy as the top European destination for migrant crossings, with close to 23,000 arrivals this year.

The European Commission is set to give Spain tens of millions of euros in emergency aid to cope with the influx from Morocco, a European source told AFP on Wednesday.