The search-and-rescue ship Aquarius, which has helped about 30,000 migrants avoid death in the Mediterranean Sea, is suspending its operations.
The humanitarian groups Doctors Without Borders (MSF) and SOS Mediterranee said European governments were forcing them to end the rescue runs.
The Aquarius has been docked in Marseille, France, since early October after Panama revoked its registration at the behest of the right-wing, anti-immigration Italian government.
The ship has been rescuing migrants who were trying to make the dangerous crossing from Libya to Europe in inadequate rafts and dinghies.
"The end of Aquarius means more lives lost at sea; more avoidable deaths that will go unwitnessed and unrecorded. It really is a case of 'out of sight, out of mind' for UK and European leaders as men, women and children perish," Vickie Hawkins, head of MSF UK, said in a statement.
The International Organization for Migration said that about 15,000 migrants have drowned in the central Mediterranean since 2013. An estimated 2,133 have died this year alone.
The Aquarius was the last rescue ship operating in the Mediterranean. Last year, five groups were running rescue ships.
At the height of the migrant influx in 2015 and 2016, NGO vessels worked alongside Italian coast guard ships.
The election of Italy's coalition government this year on an anti-migrant platform rapidly ended the cooperation, and rescue boats have been prevented from docking in Italian ports. Migrant arrivals in Italy have since fallen to pre-crisis levels following a series of hard-line measures drafted by far-right Interior Minister Matteo Salvini.
Now rescue missions fall on national coast guard crews from Europe and North Africa, who tend to return the rescued migrants to the country they set off from, usually Libya.
NGO groups describe conditions for the migrants there as "inhuman," with allegations of arbitrary detention, torture, rape and killings by human smugglers and security forces.
Henry Ridgwell contributed to this report.