They identified the men killed near the town of Beit Hanoun as members of al-Aqsa Martyrs Brigades, an armed wing of Palestinian President Mahmoud Abbas's Fatah faction.
An Israeli military spokesman had no immediate comment
Earlier on Saturday, four Palestinians were wounded, two moderately and two lightly, in an Israel Air Force strike in the northern Gaza Strip.
The IDF confirmed the air strike, saying it targeted a group of three militants.
The air strike came shortly after a Qassam rocket hit the western Negev, causing no damage or injuries.
On Friday, a rocket hit between a children's house and a nursery school in a Negev community, and two armed Palestinians were killed by IDF fire in Gaza.
There were no injuries in the rocket strike as staffers and children managed to reach shelter in time. One woman suffered from shock, however, and a nearby structure was damaged.
In Gaza, IDF soldiers shot dead a gunman in the northern part of the territory late Friday after he hurled a grenade close the border fence with Israel. Palestinian medics were allowed to retrieve his body Saturday morning.
Earlier Friday, troops opened fire on a group of gunmen during an incursion into the southern Strip, killing one and wounding two others.
Two other rockets fired by Gaza militants on Friday struck a Negev kibbutz and an open field. There were no injuries. In addition, militants fired six mortar shells at southern Israel, which exploded near the security fence in central Gaza.
Senior Palestinian Authority sources told Haaretz this week that Hamas militants who recently returned to the Gaza Strip after training in Iran have a detailed plan for upgrading the capabilities of the rockets being developed in the Strip.
The source said militants have smuggled blueprints and other detailed technical instructions into the Strip that will enable the group to develop rockets capable of striking at longer distances.