The Freedom Flotilla Coalition said its ship The Conscience was targeted at 00:23 local time on Friday and issued an SOS signal right after the attack.
The group said it had planned to sail to Gaza and "challenge Israel's illegal siege and blockade" there.
The Maltese government said everyone aboard the ship is "confirmed safe" and that a fire onboard the ship was "brought under control overnight".
The Israeli military said it was looking into reports of the attack.
The Maltese government said that 12 crew and four activists were on board the boat, while the NGO said 30 activists had been on board.
The Maltese government said a tugboat was sent to the scene to extinguish the fire, which they say was under control by 01:28 local time.
"By 2:13, all crew were confirmed safe but refused to board the tug," the statement said, adding the ship remains outside territorial waters.
AzVision.az
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