The Israeli foreign ministry did not immediately respond to a request for comment on the allegation by the Freedom Flotilla Coalition, an international non-governmental group.
The Maltese government said the vessel and its crew were secured in the early hours of the morning after a nearby tug assisted with firefighting operations, but the NGO and Swedish activist Greta Thunberg said the ship was still in danger.
Thunberg told Reuters she was in Malta and had been supposed to board the ship as part of the Freedom Flotilla's planned action in support of Gaza, which is under blockade and bombardment by Israel.
The Freedom Flotilla Coalition published video footage, filmed in darkness, showing a fire on one of its ships, the Conscience. The footage showed lights in the sky in front of the ship and the sound of explosions could be heard.
"Israeli ambassadors must be summoned and answer to violations of international law, including the ongoing blockade (of Gaza) and the bombing of our civilian vessel in international waters," it said.
The Maltese government said maritime authorities had received a mayday call from a vessel reporting a fire shortly after midnight local time. The vessel was outside territorial waters and had 12 crew members and four civilians on board, the government said.
It said a nearby tug headed to the scene and launched firefighting operations and a Maltese patrol vessel was dispatched. After several hours, the vessel and its crew were secure, it said, adding that crew had refused to board the tug.
But the Freedom Flotilla said in a statement on its website the alleged drone strikes had caused "a substantial breach in the hull".
"The drone strike appears to have deliberately targeted the ship's generator, leaving the crew without power and placing the vessel at great risk of sinking," it said.
A spokeswoman for the group, Caoimhe Butterly, said the attack took place as the ship was preparing for activists to board from another vessel. A transfer at sea had been planned rather than the ship going to harbour, for bureaucratic reasons, she said.
Thunberg said as far as she knew, the vessel was still at the location where it had been attacked.
"This attack caused an explosion and major damage to the vessel, which made it impossible to continue the mission," she said in a Zoom interview.
"I was part of the group who was supposed to board that boat today to continue the voyage towards Gaza, which is one of many attempts to open up a humanitarian corridor and to do our part to keep trying to break Israel's illegal siege on Gaza," she said.
Thunberg and the NGO said there were 30 people on board, not 16 as the Maltese government said.
Hamas issued a statement about the incident, accusing Israel of "piracy" and "state terrorism".
The Gaza war started after Hamas-led fighters killed 1200 people and took 251 hostages to Gaza in the October 7, 2023 attacks, according to Israeli tallies. Since then, Israel's offensive on the enclave killed more than 52,000, according to Palestinian health officials.
Since March 2, Israel has completely cut off all supplies to the 2.3 million residents of the enclave, and food stockpiled during a ceasefire at the start of the year has all but run out.
Another coalition ship on a similar mission to Gaza in 2010 was stopped and boarded by Israeli troops, and nine activists died. Other ships have similarly been stopped and boarded, without loss of life.
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