"Three Hamas terrorists who planned an imminent terrorist attack were eliminated" when the Israeli air force struck vehicles in the Aqaba area near Tubas, the military said.
Following the strike, "soldiers conducted a targeted raid in the vicinity of the strike, locating four weapons," it added.
The Palestinian health ministry had earlier said an Israeli strike on a vehicle in Aqaba killed two Palestinians and wounded one.
All three Palestinians were transported to a hospital in Tubas, it added, but later said Israeli forces raided the same hospital, which the army denied in a statement to AFP.
The Israeli military had earlier told AFP that the air force, "acting on intelligence, struck a terror cell that was about to carry out an attack" in the Aqaba area.
It said an army unit "was then dispatched to collect the bodies and operated in the area of the Turkish Hospital in Tubas".
However, it added, "they did not enter the hospital."
Israel often seizes the bodies of Palestinians killed during operations, particularly those who belonged to militant groups, although an AFP journalist present near the hospital at the time of the operation did not see soldiers carrying bodies.
The Palestinian health ministry said the Israeli army besieged the hospital, before breaking into it, shooting inside, "assaulting staff and patients, and arresting a number of them".
The AFP journalist in Tubas saw Israeli armoured vehicles stationed outside the hospital and soldiers deployed around it.
The journalist saw Israeli soldiers exiting the hospital and detaining staff, some of them wearing scrubs or doctor's gowns, before loading them into the armoured vehicles.
Violence in the West Bank has soared since the war in Gaza erupted on October 7 last year after Hamas's attack on Israel.
Israeli troops or settlers have killed at least 787 Palestinians in the West Bank since the start of the Gaza war, according to the Ramallah-based health ministry.
Palestinian attacks on Israelis have also killed at least 24 people in the West Bank in the same period, according to Israeli official figures.
Israel has occupied the West Bank since 1967.
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