Italian investigators suspect the vessel, chartered by MSF and the SOS Mediterranee charity and currently stuck in the French port of Marseille, passed off 24 tonnes of dangerous and potentially toxic refuse as ordinary garbage in 11 Italian ports.
Prosecutors in the Sicilian city of Catania are running the inquiry into migrant clothing, food leftovers and sanitary waste from the Aquarius and the Vos Prudence, another vessel chartered by MSF, that was handled at Italian ports last year.
Some rescued migrants are found suffering from HIV, meningitis and tuberculosis but MSF said its port operations - including waste management - have always followed standard procedures.
MSF’s Marco Bertotto told RFI the claims were “grotesque”.
“We have carried out more than 200 landings under very tight control of the police. It’s unimaginable in that context that we would have conducted fraudulent activities that could damage human health. It’s grotesque."
MSF says it will appeal the verdict through the Italian courts.
The Aquarius is docked in Marseilles, France, out of reach of the Italian authorities for the moment. But prosecutors in Catania said it would be seized if it disembarked to Italy.
The Aquarius has been stuck in Marseilles since the Panamanian authorities revoked its flag, following alledged complaints by the Italian authorities.
In September, Matteo Salvini, Italy’s far-right deputy prime minister, declared that the Aquarius would "never see an Italian port" again.
He praised the seizure order for the Aquarius tweeting: “It seems I did well to close the Italian ports to the NGOs.”
In October thousands of people demonstrated in France in support of the Aquarius.