It uploaded video footage showing a fire on one of its ships but did not indicate who could have been responsible for the attack.
"The drone attack appears to have specifically targeted the ship's generator, and the vessel is now at risk of sinking with 30 international human rights activists on board," the NGO said in a social media post.
The ship issued an SOS distress call after being hit 32km east of Malta, to which Cyprus responded by dispatching a vessel, the charity said.
The Maltese government later said everyone aboard the ship was "confirmed safe".
"The vessel had 12 crew members on board and four civilian passengers; no casualties were reported," the statement said, adding that a nearby tug had been directed to aid the vessel," it said in a statement.
"The tug arrived on scene and began firefighting operations. By 1:28am (local time), the fire was reported under control. An Armed Forces of Malta patrol vessel was also dispatched to provide further assistance," the government said.
"By 2.13am, all crew were confirmed safe but refused to board the tug ... The ship remains outside territorial waters and is being monitored by the competent authorities."
The coalition is campaigning to end Israel's blockade of Gaza.
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.
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.
