Military officials said a fifth militant aboard the boat was missing, Haaretz reported.
An Israeli aircraft fired a missile at a target in northern Gaza, killing one person, Palestinian officials said.
Concerning the sea assault, sources in Gaza told Haaretz the men were members of the al-Aqsa Martyrs Brigade, an extremist branch of the Fatah faction led by Palestinian Authority President Mahmoud Abbas.
The militants were training for a seaborne attack on Israel when they came upon Israeli forces, the sources said.
Israeli military officials said no troops were injured.
An Israeli military official told Army Radio the sea operation would be a boost for the navy's elite commando unit, Shayetet 13, which created a storm of international criticism by killing nine activists in a raid on a Gaza-bound humanitarian aid flotilla a week ago.
"This will be a shot in the arm for the commandos after the hard week they have been through," the official said.