Another 20 were wounded, according to the Palestinian Health Ministry.
The overnight raid in the old city, or kasbah, of Nablus, was one of the deadliest in the West Bank in 2022 and comes at a time of escalating conflict.
The target of the raid was a group of Palestinian gunmen calling themselves the Lions' Den. The group was responsible for the recent fatal shooting of an Israeli soldier and several attempted attacks, the army said.
The five men killed in the raid were in their 20s and 30s, the Health Ministry said. One of those killed, Wadie Houh, was reportedly a leader of the group. Several of the wounded were in serious condition, the ministry said.
Ongoing Israeli arrest raids in the West Bank pose a serious challenge to the Palestinian self-rule government, which administers just over one-third of the territory.
Palestinian President Mahmoud Abbas relies on security cooperation with Israel, particularly against his Islamic militant rivals, to remain in power. At the same time, this cooperation is deeply unpopular among Palestinians who chafe against Israel's open-ended occupation, now in its 56th year.
Younger Palestinians are particularly disillusioned. Small bands of gunmen have formed in some areas, first in the Jenin refugee camp, a stronghold of militants, and now in Nablus. These groups challenge the Palestinian Authority and carry out attacks against Israeli targets.
In Tuesday's raid, Israeli forces blew up an explosives lab in an apartment in Nablus, the military said. The statement said a number of militants were targeted and noted that Palestinians were reporting casualties. From the wording of the statement it was not immediately clear if some of those killed and wounded were hit in an initial ambush rather than a subsequent firefight.
Abbas' spokesman, Nabil Abu Rdeneh, issued a statement in which he described the ongoing Israeli raids as a war crime.
More than 125 Palestinians have been killed in Israeli-Palestinian fighting in the West Bank and east Jerusalem this year. The fighting has surged since a series of Palestinian attacks killed 19 people in Israel in the spring. The Israeli army says most of the Palestinians killed have been militants. But stone-throwing youths protesting the incursions and others not involved in confrontations have also been killed.
Israel captured the West Bank in the 1967 Mideast war and has built more than 130 settlements there, many of which resemble small towns, with apartment blocks, shopping malls and industrial zones. The Palestinians want the West Bank to form the main part of their future state. Most countries view the settlements as a violation of international law.
