Hospital staff said 14 people were killed in the incident in the Nuseirat refugee camp.
The building was a former school run by the United Nations Relief and Works Agency for Palestine Refugees in the Near East (UNRWA).
UN spokesman Stéphane Dujarric said in New York that UN properties should never be attacked nor used by military groups.
A spokesman for the Israeli air force said it hit a Hamas command and control post in Nuseirat after taking measures to minimise the risk of harming civilians.
The UN condemned the attack on the former school run by the United Nations Relief and Works Agency. (EPA PHOTO)
Earlier, the Israeli military said two soldiers were killed when a rescue helicopter crashed in the Gaza Strip.
It said seven others were injured and transported to a clinic for treatment.
The Yanshuf helicopter belonging to the Israeli air force was on a mission to evacuate an injured soldier to a hospital for medical treatment. It crashed while landing in the Rafah area in Gaza, the Israel Defence Forces (IDF) said.
An initial inquiry indicated the crash was not caused by enemy fire, the IDF said, noting the incident was still under investigation.
Elsewhere Israeli forces killed at least six Palestinians in separate incidents in the occupied West Bank.
An air strike in the city of Tubas killed five men the military said were armed with explosives that posed a threat to Israeli forces and destroyed weapons production facilities as well as a vehicle rigged with explosives and a remote control.
The Palestinian Red Crescent said rescue crews had recovered five bodies at the site and had transferred them to hospital.
In a separate incident in the city of Tulkarm, the military said troops backed by police and intelligence services killed an armed militant.
There was no immediate confirmation from any of the armed Palestinian factions that the men killed in the operation were their fighters.
Entrances and exits from Tubas were sealed off and Israeli military vehicles, including road diggers and armoured personnel carriers, could be seen moving through the city, close to the border with Jordan at the northern end of the West Bank.
Israeli carried out air strikes on the city of Tulkarm. (EPA PHOTO)
On Wednesday, as the operations were going on, the military reported a ramming attack east of Ramallah in the West Bank in which it said the driver of a fuel tanker accelerated towards Israeli soldiers before being shot.
An Israeli soldier was killed in the incident, the military said.
Israeli forces have been conducting a series of operations in the northern West Bank for the past two weeks, with extended raids in Tubas, Jenin and Tulkarm.
All three cities have a heavy presence of armed factions including Hamas, Islamic Jihad and Fatah.
Violence has surged in the West Bank since the start of the war in the Gaza Strip, with almost daily sweeps by Israeli forces that have involved thousands of arrests and regular gunbattles between security forces and Palestinian fighters.
More than 680 Palestinians have been killed in the West Bank since the Hamas-led attack on Israel on October 7 last year, including both fighters and unarmed civilians, according to the Palestinian health authorities.
In the same period, about 40 Israeli troops and civilians have been killed in attacks by Palestinians or in clashes with fighters, according to figures from Israel's domestic security agency.
The war began after the October 7 attacks by Hamas, when the militia and others killed 1200 people in Israel and took some 250 hostage in Gaza.
with DPA
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