The deaths brought to 13 the number of Palestinians killed by the military in Gaza since the army launched its latest ground incursion early Thursday, concentrated in the southern part of the territory.
The three militants loyal to ruling Islamist movement Hamas - including a local leader in the military wing - were killed in an airstrike on their vehicle in the northern town of Beit Lahiya, a local medic and witnesses said.
The Israeli military confirmed an attack on a vehicle that it said was transporting weapons. Medics said that another five Palestinians were wounded.
Hamas' Ezzedine Al Qassam Brigades was one of three groups to claim the June 25 abduction of an Israeli soldier that sparked a wider four-month offensive in the Gaza Strip where around 250 Palestinians have died since then.
On Friday, a 29-year-old woman was shot dead by soldiers operating in the south and another Palestinian died overnight from wounds suffered during an airstrike against the house of a Hamas militant.
The army has said that its latest operation was targeting "tunnels and other terror threats."
A spokesman said that troops had killed one of two gunmen in southern Gaza, but when questioned about the death of a woman, he said only that the army had "heard such claims" and was "checking."
Israel's prolonged operations in Gaza have the stated goals of retrieving captured Corporal Gilad Shalit and stopping militant rocket attacks on the Jewish state.
Since the offensive began June 28, around 250 Palestinians and two Israeli soldiers have died in the Gaza Strip.
Internal Palestinian tensions have also soared amid deadlocked efforts to form a national unity government as a means to ending unprecedented financial and political crisis since Hamas formed a government last March.
Twenty Palestinians were wounded in overnight clashes between supporters of Hamas and President Mahmoud Abbas' moderate Fatah party in Beit Lahiya, mostly sustaining gunshot wounds and injuries from exploding grenades, a medic said.
The violence - at a time of increased tensions between rival Palestinian factions - came one day after an officer in the intelligence service loyal to Abbas and a Hamas official were shot dead in Gaza City.
The Islamists have stubbornly rejected immense pressure from Abbas and the international community to accept a political program that amounts to recognition of Israel and past Israeli-Palestinian agreements.
In Damascus, the exiled political supremo of the movement called on Arab and Palestinian leaders to hold a summit to ask for a Palestinian state to be built on Palestinian territory occupied by Israel in 1967.
"We can do it. Israel will not be able to scupper this project," Khaled Meshaal told Palestinian leaders.
He has accused Israel of refusing to free prisoners in exchange for the release of Shalit.
Israeli officials say that Meshaal, who famously escaped a Mossad assassination bid in 1997 in Amman, is a marked man for allegedly ordering the capture of 20-year-old conscript.
© 2006 Agence France-Presse