“Three Palestinians have been killed by Israeli bullets in Nablus,” the ministry said, adding the identities of those killed in the northern West Bank city were still unknown.
The Israeli army said three “armed terrorists” had opened fire on its soldiers from a vehicle in a Nablus neighbourhood and the troops fired back “to neutralise” them.
The soldiers recovered three M-16 rifles, a gun, cartridges and other military equipment, the army said in a statement.
The Palestinian president’s spokesman, Nabil Abu Rudeineh, said Tuesday’s killing of the three Palestinians amounted to a “war crime”.
“Israeli crimes will not bring our people to their knees, and will not bring security and stability to anyone,” he said in a statement.
Israel has occupied the West Bank since the Six-Day War of 1967.
Since early last year, the territory has seen a string of attacks by Palestinians on Israeli targets, as well as violence by Israeli settlers against Palestinian communities.
Violence linked to the Israeli-Palestinian conflict this year has killed at least 201 Palestinians, 27 Israelis, one Ukrainian and one Italian, according to an AFP tally compiled from official sources on both sides.
They include, on the Palestinian side, combatants as well civilians and, on the Israeli side, three members of the Arab minority.
Excluding Israeli-annexed east Jerusalem, the West Bank is home to nearly three million Palestinians, as well as around 490,000 Israelis who live in settlements considered illegal under international law.