Israeli air strikes hit Hamas military sites in the Gaza Strip on Saturday in response to rocket fire from the Palestinian enclave run by the Islamist movement, the Israeli army said.

"A short while ago, in response to the rocket attack, (Israeli military) aircraft struck a number of Hamas terror targets in the Gaza Strip," the army said in a statement.

The strikes came after Hamas "launched a rocket... toward Israeli civilians in southern Israel", it said, adding the projectile was intercepted by Israel's air defences.

The Israeli "aircraft targeted a weapons manufacturing site located inside a Hamas military post and an additional three military posts belonging to Hamas," the statement said.

Balls of flame shot into the air, leaving dark smoke drifting over the territory, after the strikes.

The army said hours earlier that air raid sirens were sounded in the southern Israeli city of Ashkelon and in areas near the blockaded Gaza Strip.

The exchange came after three Palestinians were killed and 12 others wounded on Friday during an Israeli army raid in Jenin, a stronghold of armed Palestinian factions in the occupied West Bank.

The men were killed when Israeli forces opened fire on a vehicle in which they were, the Palestinian news agency Wafa said.

Israel's army said soldiers had come under fire during an operation to search for weapons.

One of the dead was a Hamas commander, the group said, vowing that the killings "will not go unpunished".

In April, Israeli warplanes also hit Gaza after incoming rocket fire. The Hamas-controlled Gaza coastal enclave of 2.3 million people has been under an Israeli blockade since 2007.

That exchange came after nearly a month of deadly violence focused on Israeli-annexed east Jerusalem's flashpoint Al-Aqsa mosque compound, the third holiest site in Islam.

Last year, Israel and Hamas fought an 11-day war triggered in part by unrest over the Al-Aqsa mosque compound, the most holy site for Jews, who call it the Temple Mount.

Israel occupied the West Bank and east Jerusalem in the 1967 Six-Day War. It later annexed east Jerusalem in a move never recognised by most of the international community.