Italian authorities have ordered the seizure of the migrant rescue ship Aquarius after claiming that discarded clothes worn by the migrants on their voyage from Libya to Italy could have been contaminated by HIV, meningitis and tuberculosis.

Prosecutors from Catania, eastern Sicily, alleged that the waste was illegally labelled by the ship’s crew as “special waste” rather than “toxic waste”.

The Aquarius is currently docked in Marseilles, France, where so far it is beyond the reach of the Italian authorities.

The ship is operated by the charity Médecins Sans Frontières (MSF) and SOS Méditerranée. Prosecutors in Catania said: “If Aquarius would disembark to Italy, it will be immediately put under seizure.”

Nevertheless, the Italian authorities have placed 24 people under investigation for ‘‘trafficking and the illegal management of waste,” including the captain of the Aquarius, Evgenii Talanin, and Michele Trainiti, deputy head of the Italy mission of MSF Belgium. The Sicilian prosecutors also fined MSF a total of €460,000 (£409,000) and froze some of its bank accounts based in Italy.

A total of 24 tonnes of discarded material – including leftover food and medical materials as well as clothes – was being investigated.

Aids campaigners criticised the prosecutors’ claims that clothing could have been contaminated with HIV. “Clothing categorically is not, and has never been, an HIV transmission risk,” said Deborah Gold, chief executive of the National AIDS Trust.

“This would have stood out as ridiculous even amongst the misinformation of the 1980s, never mind in 2018. Migrants and people seeking asylum have historically been attacked using myths about HIV and infectious conditions, and we condemn this both for its stigmatising of people living with HIV and of migrants fleeing hardship.”

The Aquarius has been stuck in Marseilles since the Panamanian authorities revoked its flag, after “complaints by the Italian authorities”. But the ship seemed to have reached an agreement with a country that would offer the NGO its flag and was ready to leave the French port in few days to reach the waters of Libya.

Matteo Salvini, Italy’s far-right deputy prime minister, hailed the seizure order for the Aquarius, tweeting: “It seems I did well to close the Italian ports to the NGOs.”

NGO rescue boats have almost all disappeared from the central Mediterranean since Salvini announced soon after taking office that he was closing Italian ports to non-Italian rescue vessels.

The chief prosecutor of Catania, Carmelo Zuccaro, who is leading the investigation against the Aquarius and who is known for having launched several investigations against the rescue boats operated by aid groups, has recently dropped the charges for illegal detention and kidnapping against Salvini, after the minister of the interior was placed under investigation for preventing the disembarkation of migrants from the coastguard ship Ubaldo Diciotti, last August.

In a statement released on Tuesday, MSF described the allegations against the Aquarius crew as “disproportionate and unfounded, purely aimed at further criminalising lifesaving medical-humanitarian action at sea’’.

“After two years of defamatory and unfounded allegations of collusion with human traffickers against our humanitarian work, we are now accused of organised crime aimed at illicit waste trafficking. This latest attempt by the Italian authorities to stop humanitarian lifesaving search and rescue capacity at any cost is sinister” says Karline Kleijer, MSF’s head of emergencies.

“This is another strike in the series of attacks criminalising humanitarian aid at sea. The tragic current situation is leading to an absence of humanitarian search and rescue vessels operating in the central Mediterranean, while the mortality rate is on the rise,” said Frédéric Penard, SOS Méditerranée’s head of operations.

People seeking asylum are still attempting the risky crossing but, without the rescue boats, the number of shipwrecks is likely to rise dramatically.

The death toll in the Mediterranean has fallen in the past year, but the number of those drowning as a proportion of arrivals in Italy has risen sharply in the past few months, with the possibility of dying during the crossing now three times higher.

According to the International Organization for Migration, so far in 2018 more than 21,000 people have made the crossing and 2,054 have died.

Amnesty International says that about 20,000 asylum seekers were intercepted by Libyan coastguards in 2017 and taken back to Libya’s detention camps, where, according to human rights organizations, they face torture and violence.

According to sources in Libya and aid groups, on Tuesday the Libyan coastguard and security forces forced more than 70 migrants off a cargo ship they had been on for 10 days.

They were rescued by the ship’s crew on 10 November while attempting the crossing to reach Sicily, but the Libyans had ordered the captain of the cargo ship to send them back to Misrata.

The migrants had refused to disembark from the merchant ship Nivin off the coast of Misrata in Libya, for fear of being sent back to Libyan detention camps.

According to sources confirmed by aid groups, Libyan coast guards “shot rubber bullets at the asylum seekers on board and 10 people were injured. The others were sent back to the detention center, including several minors.”