The PRC said that its General Secretary, Zohair al-Qaisi was one of two Palestinians killed in the strike, along with fellow-member Mahmud Halani, hours after Palestinians fired mortar rounds into Israel.
Medical officials told AFP that a third man man was seriously injured in the attack, on a car travelling in the Tel el-Hawa neighbourhood, west of Gaza City.
An army spokeswoman confirmed air force "activity" in Gaza but did not immediately have further details.
Israeli security officials speaking on condition of anonymity said that one of the dead men was a senior militant leader.
Palestinian militants in the Gaza Strip fired two projectiles into southern Israel earlier Friday without causing any casualties or damage, the military said.
A spokeswoman initially said they were rockets, but army radio later referred to them as mortar shells.
Hamas, which rules the Gaza Strip, has maintained a tacit truce with Israel, but other armed Palestinian groups regularly fire rockets and mortars across the border, which can spark air strikes in response.
The relatively small Popular resistance Committees is one of the most active.
"We are not committed to the truce, we will respond very strongly to this (Israeli) crime," Abu Ataya a spokesman for the PRC's military wing, the Al-Nasser Brigades, told AFP.
Before Friday's air strike Israeli army radio quoted what it called "senior military sources" as saying the army "does not intend to allow the firing to continue."
On Wednesday Israeli troops entered northern Gaza, briefly sealing the Erez border crossing between the Palestinian territory and Israel, Hamas officials said.
The Israeli military said that "the army entered the area to stop terrorist activities."
Israeli troops regularly carry out brief incursions into the Gaza Strip, despite formally withdrawing from the territory in 2005.
They usually enter the Palestinian territory to raze homes or trees near the border that they claim are used by militants trying to infiltrate Israel, fire rockets or plant explosives along the border area.