Everyone aboard an aid flotilla for Gaza that was hit by drones in international waters off Malta overnight are "confirmed safe," the Maltese government said in a statement on Friday.

"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.

The group organising the aid boat for Gaza said it was attacked on Friday by Israeli drones in international waters off Malta as they headed towards the Palestinian territory.

"At 00:23 Maltese time, the Conscience, a Freedom Flotilla Coalition ship came under direct attack in international waters," the group said in a statement.

Israel has not commented on the allegation.

(With input from agencies)