The Aquarius migrant rescue ship is to end its operations in the Mediterranean, the humanitarian groups that chartered the boat said.
The vessel has been stranded in Marseille since early October after Panama revoked the right to fly its flag following a request from the Italian government.
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.
"This is the result of a sustained campaign, spearheaded by the Italian government and backed by other European states, to de-legitimise, slander and obstruct aid organisations providing assistance to vulnerable people," Doctors Without Borders (MSF) said in a statement.
"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".
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.
The ships have rescued thousands of migrants from the Mediterranean with immigration a hot-button issue in the European Union.
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, while other European nations have closed their borders.
Italy's former centre-left government tried to stem the flow of migrants by working with the Libyan authorities and limiting the NGO effort.
Anti-immigrant Deputy Prime Minister and Interior Minister Matteo Salvini, who came to power as part of a populist government in June, however, has since closed Italian ports to civilian and military boats that have rescued migrants, saying Italy bears an unfair share of the migrant burden.