The World Health Organization said four children were among six people wounded on Saturday in a strike on a polio vaccination centre in northern Gaza.
The WHO only restarted the second round of vaccinations in northern Gaza on Saturday after being forced to suspend them earlier because of Israeli bombardments.
WHO chief Tedros Adhanom Ghebreyesus said the health centre was "in an area where a humanitarian pause was agreed to allow vaccination to proceed" and the attack could off parents of children needing a second vaccine to be covered.
The Gaza civil defence agency source told AFP that it was "an Israeli quadcopter that fired two missiles which hit the wall of Sheikh Radwan clinic".
Israel rejected the claim that one of its drones fired missiles at the centre, despite being responsible for attacking and besieging several Gaza hospitals, and has killed scores of medical staff.
An Israeli military statement said: "The IDF (army) is aware of claims regarding the injury of Palestinian civilians in the Sheikh Radwan vaccination center in the northern Gaza Strip."
It added: "Contrary to the claims, an initial review determined that the IDF did not strike in the area at the specified time."
"We have received an extremely concerning report that the Sheikh Radwan primary health care centre in northern Gaza was struck today while parents were bringing their children to the life-saving polio vaccination in an area where a humanitarian pause was agreed," Tedros said.
"Six people, including four children, were injured," he added.
The Israeli military has been pounding northern Gaza for weeks in a major offensive, killing hundreds of people over the past month, devastating the area by tightening its siege and displacing the region's inhabitants.
UN agency chiefs have also spoken of an "apocalyptic" situation in north Gaza which has been "denied basic aid and life-saving supplies".
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, Tedros 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.
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 five.
Israel's military campaign, ongoing for over a year, has killed 43,314 people in Gaza, including women and children. Israel's atrocities have been called a 'genocide' and 'war crimes' by UN agencies, experts and NGOs.