The MSF vessel was stranded in Marseille, in the south of France, since October after Panama revoked the right to fly its flag following a request from Italy's far-right, anti-establishment government.
The charity-run migrant rescue ship Aquarius will end its missions in the Mediterranean, with humanitarian group MSF blaming Italy and other European states for smearing and obstructing its work.
The vessel, chartered by SOS Mediterranee and Doctors Without Borders (MSF), has been stranded in Marseille, in the south of France, since October after Panama revoked the right to fly its flag following a request from Italy's far-right, anti-establishment government.
The ship became a symbol of the diplomatic crisis surrounding the arrival of migrants in Europe when Italy slammed shut its ports in June and left the ship stranded with 630 people on board.
Aquarius has helped almost 30,000 migrants at sea who have attempted the perilous journey across the Mediterranean.
"This is the result of a sustained campaign, spearheaded by the Italian government and backed by other European states, to delegitimise, slander and obstruct aid organisations providing assistance to vulnerable people," MSF said in a statement Thursday.
"Coupled with the EU's ill-conceived external policies on migration, this campaign has undermined international law and humanitarian principles. With no immediate solution to these attacks, MSF and SOS Mediterranee have no choice but to end operations by the Aquarius," it added.
SOS Mediterranee director of operations Frederic Penard said "giving up the Aquarius has been an extremely difficult decision" but added that the group was "actively exploring options for a new boat".
Last month Rome also ordered the seizure of the Aquarius, which had been conducting rescue operations off Libya since 2016, for allegedly dumping toxic waste.
According to Italian media, investigators suspect the vessel passed off 24 tonnes of potentially toxic waste as ordinary waste.
Prosecutors in the Sicilian city of Catania are running the inquiry into migrant clothing, food leftovers and sanitary waste that was handled at Italian ports from the Aquarius and the Vos Prudence, another vessel chartered by MSF last year.
- 'Excellent news' -
Aquarius began its rescue operations off Libya in February 2016 flying the flag of Gibraltar, and later Panama.
But it hit rocky waters in June this year when it attempted to dock in Corsica with 630 migrants on board, only for Italy's new populist government to shut its ports to civilian and military boats that have rescued migrants -- saying Italy bears an unfair share of the migrant burden.
After also being refused by Malta, the ship finally landed in Valencia in Spain after other EU states promised to take in some of the migrants.
It was the first of a series of similar incidents that triggered divisions in the EU over how to tackle migration and its impact on frontline member states Italy, Greece and Spain.
The EU is trying to boost its defences against future migrant surges after having sharply reduced arrivals since a 2015 peak as a result of cooperation with Turkey and Libya.
The International Organisation for Migration says that about 15,000 migrants have drowned in the central Mediterranean since 2013.
During the same period Italy has seen 600,000 migrants land on its coastline.
Marine Le Pen, the head of France's right-wing National Rally, tweeted her joy at the news that Aquarius was stopping its operations.
"The end of the pro-migrant activities of Aquarius, an accomplice of trafficking mafias, is excellent news."