Medicins San Frontiers was forced to complete the search and rescue operations on the deadly migration route of the central Mediterranean.
The charity organization and its partner SOS Méditerranée said that Europe "will condemn people to drown" and accused the Italian government of a smear campaign aimed at preventing and discrediting rescue operations in the Mediterranean.
"This is a dark day," said Nelke Manders, Director General of MSF.
"Not only has Europe failed to provide search and rescue capabilities, it has also actively sabotaged other people's attempts to save lives: the end of Aquarius means more deaths at sea and more unnecessary deaths that will go empty ".
About 2,133 people are believed to have died in the Mediterranean this year, most of them starting with dangerous and overcrowded vessels from Libya hoping to reach Europe.
The Aquarius, which since 2016 has assisted about 30,000 people, was the last ship to help the affected migrants in the region, after some violations by the Italian government forced many others to stop operations.
Since she was rescued by 58 people more than two months ago she was berthed at the port of Marseille after being stripped of her Panamanian registration.
Now he faces accusations of criminal activity, with the Italian government investigating the ship for trafficking in human beings and the illegal treatment of toxic waste.
In recent months, ships carrying migrants have found it impossible to dock in ports in Italy and Malta, and many have been left floating in the sea for weeks or forced to return to Libya.
Italian Minister of the Interior, Matteo Salvini, said that other European countries must accept migrants arriving in Italy and threatened to return them to Libya.
"Europe must seriously decide to help Italy in concrete terms," he said in August.
For other European states, prevention of people who reach their shores is also a priority.
EU member states support Libyan authorities to intercept boats and repatriate migrants to Libya, where they are located face the continued danger in the fields where torture, rape and slavery are widespread.
MSF argues that this constitutes support for forced returns while "claims success" on migration.
"Let's say clearly what it means success: lack of life-saving assistance at sea, children, women and men turned away from arbitrary detention with virtually no hope of escape," said Karline Kleijer, MSF's emergency manager.
"As long as people suffer at sea and in Libya, MSF will look for ways to provide them with the medical and humanitarian care they desperately need."
The International Organization for Migration states that 15,000 migrants have drowned in the central Mediterranean since 2013.