Of the four vessels still remaining, two support ships turned back, while the vessel Marinet continued sailing toward Gaza but was still far away after a late arrival due to technical malfunctions, it added.
The flotilla, loaded mainly with humanitarian aid and medical supplies, set sail at the end of August. It was the first time in years that around 50 ships sailed together toward Gaza, carrying hundreds of civilian supporters.
Israel has maintained a blockade on Gaza, home to nearly 2.4 million, for nearly 18 years, and further tightened the siege in March when it closed border crossings and blocked food and medicine deliveries, pushing the enclave into famine.