Israeli forces killed two Palestinians, including an Islamic Jihad commander, in the West Bank city of Nablus on Tuesday in the first fatal raid since a ceasefire took hold in the Gaza Strip last week.

Islamic Jihad threatened to launch attacks inside Israel to avenge the death of Tarek Juma Abu Ghali, whom the militant group described as one of its most senior commanders in the northern West Bank.

A second Palestinian, affiliated with the Islamist militant group Hamas, was also killed in the overnight raid, Palestinian security sources said.

The killings, which were confirmed by the Israeli army, could test the fragile ceasefire that took effect last Thursday between Israel and militants in the Hamas-controlled Gaza Strip.

"Calm in Gaza does not mean that we will sit in our seats waiting to be slaughtered one by one," Islamic Jihad said in a statement. "This crime will not pass without punishment and the coming days will be a witness to that."

Hamas, which claimed responsibility for a shooting attack that injured three Israeli hikers near a West Bank settlement on Friday, also called on Palestinian groups in the West Bank to retaliate for the killings, saying they had a right to do so because the ceasefire deal was limited to the Gaza Strip.

Western-backed Palestinian Prime Minister Salam Fayyad departed from his prepared remarks at a security conference in Berlin to condemn the Nablus raid.

"This is the kind of activity that has to stop, and has to stop promptly, if we are going to be able to succeed," Fayyad said. "Our own political credibility will continue to be at stake as long as those kinds of incursions continue."

The Berlin conference is meant to bolster Palestinian police forces so they can assume greater security responsibilities in the Israeli-occupied West Bank.

Officials on both sides doubt the truce in the Gaza Strip will last.

The army on Tuesday confirmed that Palestinians fired a mortar shell into Israel from Gaza overnight in the first reported violation by militants of the ceasefire.

No one was hurt by the mortar shell and there was no immediate claim of responsibility.

Hamas official Sami Abu Zuhri said his group was not aware of the incident and remained committed to the truce.

An Israeli army spokesman said the Islamic Jihad commander killed in Nablus had directed "terrorist squads" and was involved in making explosive devices.

Nablus Governor Jamal Muheisen called the Israeli raid in the city an "unjustified crime" but said he did not believe it would threaten the Gaza truce.

Under the ceasefire deal, brokered by Egypt, Hamas agreed to prevent other militant groups in the Gaza Strip, including Islamic Jihad, from launching cross-border attacks.

Israel also agreed to halt fighting in the Gaza Strip and to gradually relax its economic blockade on the enclave.

Security forces loyal to Palestinian President Mahmoud Abbas deployed in Nablus late last year as part of a Western-backed law-and-order campaign. But Palestinian officials say frequent Israeli raids into the city have undermined that effort.