WHO chief Tedros Adhanom Ghebreyesus, said in a message on X, that the UN agency had received "an extremely concerning report" that the centre "was struck today while parents were bringing their children to the life-saving polio vaccination" drive.
Without naming who carried out the strike, he said the Sheikh Radwan primary health care centre was "in an area where a humanitarian pause was agreed to allow vaccination to proceed."
"Six people, including four children, were injured," he added.
The Israeli military has been pounding northern Gaza in recent weeks as part of its campaign to crush the Hamas militant movement in retaliation for the militants' attacks against Israel on October 7, 2023.
The WHO launched a needed second round of child polio vaccinations in northern Gaza on Saturday after Israeli bombing halted the drive.
The vaccination drive began on September 1 with a successful first round, after the besieged Palestinian territory confirmed its first case of polio in 25 years.
"A WHO team was at the site just before" Saturday's strike, Ghebreyesus said.
"This attack, during humanitarian pause, jeopardises the sanctity of health protection for children and may deter parents from bringing their children for vaccination," he added.
"These vital humanitarian-area-specific pauses must be absolutely respected," he said, calling for a ceasefire in the territory.
The WHO says some 119,000 children in the north are awaiting a second dose, while 452,000 have been vaccinated in central and southern Gaza.
Typically spread through sewage and contaminated water, poliovirus is highly infectious.
It can cause deformities and paralysis, and is potentially fatal, mainly affecting children under the age of five.
Hamas's 2023 attack resulted in the deaths of 1,206 people, mostly civilians, according to an AFP tally of Israeli official figures.
Israel's retaliatory military campaign has killed 43,314 people in Gaza, most of them civilians, according to figures from the Hamas-run territory's health ministry which the UN considers reliable.
