Italy has ordered the seizure of the migrant rescue ship Aquarius for allegedly dumping potentially toxic waste, Doctors without Borders (MSF) said Tuesday, in a fresh blow for aid groups working in the Mediterranean.

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Investigators accuse the vessel of passing 24 tons of dangerous and potentially toxic refuse off as ordinary garbage in 11 Italian ports, Italian media reported.

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.

Some rescued migrants were found to be suffering from HIV, meningitis and tuberculosis but MSF said its port operations "including waste management, have always followed standard procedures." "The relevant authorities have not contested these procedures or identified a public health risk since we started our activities at sea," it said.

"This is another strike in the series of attacks criminalizing humanitarian aid at sea," said Frederic Penard, SOS Mediterranee's operations head. "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."

French authorities have not commented so far. According to SOS Mediterranee, the crew has not received any official notice yet.

MSF bank accounts in Italy have been blocked by the authorities, the international charity said. Twenty-four people are under investigation, Italian news agency ANSA quoted sources as saying.

Rescue ships have saved thousands of migrants stranded in the Mediterranean.

"The only crime we see today on the Mediterranean is the total dismantling of the search and rescue system," said MSF Italy director Gabriele Eminente.

He added in the statement that MSF had suffered "two years of defamatory campaigns" against non-governmental organizations.

Aquarius has been in Marseille since Panama revoked the right to fly its flag following a request from Italy's far-right, anti-establishment government, meaning the Aquarius cannot legally set sail.

Frontline state Italy has clamped down on asylum-seekers under far-right Interior Minister Matteo Salvini who calls non-profit organizations rescuing migrants from sea "smuggler helpers."

The International Organization for Migration says that about 15,000 migrants have drowned in the central Mediterranean since 2013.