Italy has called for the seizure of the Aquarius migrant rescue ship, alleging it illegally dumped 24 tonnes of potentially toxic waste in its ports.
One of two charities that lease the Aquarius, Doctors Without Borders (MSF), condemned the measure as "unfounded and sinister".
The Aquarius is involved in a long-running feud with Italy over its rescue operation in the Mediterranean.
It has rescued thousands of migrants but is currently docked in Marseille.
It has been stuck in the French port for months since Panama revoked its registration - citing intense political pressure from Italian authorities. It has since had trouble maintaining stable registration status, and a de-flagged vessel cannot legally set sail.
What are the latest allegations?
MSF says this disagreement centres around waste management of items such as food leftovers, clothes, and medical waste.
Prosecutors in Sicily say 24 tonnes of potentially hazardous waste were dumped over a period of two and a half years in 11 ports, of which five are in Sicily.
According to Italian reports, clothing from migrants with infectious diseases were not properly disposed of and 24 people have been identified as suspects in the case.
The investigation is also thought to involve another MSF ship, the Vos Prudence, which ceased search and rescue work more than a year ago.
MSF insists its ships have always followed standard procedures in port, and that no questions over its waste management were raised by port authorities during its time searching the seas over the past three years.
⚡PRESS STATEMENT: @MSF is submitting an appeal to Italian review courts. We are fully willing to cooperate with authorities, but refute accusations that MSF was involved in criminal activity aimed at illicit waste management of any kind. #Aquarius https://t.co/XrkhtE8jpq— MSF Sea (@MSF_Sea) November 20, 2018
Instead, it alleged that the charges were politically motivated.
"After two years of defamatory and unfounded allegations of collusion with human traffickers, judicial investigations, and bureaucratic obstacles against our humanitarian work, we are now accused of organised crime aimed at illicit waste trafficking," MSF said in a statement.
Why Aquarius has riled Italy's populist government
The Aquarius, which is chartered by both MSF and the migrant rescue charity SOS Mediterranée, came to worldwide attention over the summer as Italy closed it ports to migrant rescue ships, leaving the ship stranded at sea with people rescued from the water.
Hundreds of migrants rescued by the Aquarius were eventually allowed to disembark in the Spanish port of Valencia in June, after being turned away by Italy and Malta.
Italy's interior minister Matteo Salvini, who has long criticised the migrant rescue operations, has accused the charities of collaborating with human traffickers operating out of Libya to run a "taxi service" to Italian ports.
The Catania prosecutor involved in the latest investigation, Carmelo Zuccaro, has himself suggested in the past that NGOs have had direct contact with traffickers.
Italian policy is that migrants discovered at sea should be returned to Libya by that country's coast guard.
Reacting to the Sicilian decision to order the ship's seizure, he said on Twitter: "I was right to block the NGO ships".
"I stopped not only the traffic of illegal immigrants but, so it appears, blocked smuggling of toxic waste," he said, adding the hashtag "ports closed".