UNRWA's Director of Planning Sam Rose has called on Hamas and Israeli authorities "not to misuse" the organisation's schools.
It comes after the Civil Defence Agency said that 15 people were killed in a strike on a school sheltering displaced people.
The Israeli military said it had targeted "terrorists".
Speaking on RTÉ’s Morning Ireland, Mr Rose said: "It is hard to see how any of this is justified in terms of attacks that are causing large losses of life in the past few days on almost a daily basis.
"Civilians are civilians, wherever they are, even if Hamas is endangering them."
Regarding reports that Hamas militants are sheltering inside schools, Mr Rose said UNRWA has "strict rules, strict policies forbidding anyone with weapons, police or civilian police when they are armed from entering our premises".
"If indeed that has happened, it's something and it's a claim that we take extremely seriously and it's something that we, as the United Nations, we insist against it," he said.
"But we don't have the ability always to investigate it ourselves, particularly not during a conflict such as this," he added.
He said UNWRA is "aware of the reports", adding the organisation takes such reports "very seriously".
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Mr Rose said that the attack on the Abu Araban site in central Gaza's Nuseirat camp is one of five in the past 10 days targeting schools, three of which were UNRWA schools.
The UNWRA official said schools are being used as shelters, adding that education is on hold at the facilities.
He said: "We run about 300 schools in Gaza, normally educating 300,000 young children from age 5 to 15.
Mr Rose said that "since October those schools have been operating as shelters" with each school sheltering several thousand people, who are living in classrooms, the courtyards and "then lots of people living in the surrounding areas".
He described the schools as "very built up" and "very overcrowded".
Mr Rose warned that "education is stopping" as a consequence of people sheltering inside the complexes.
In relation to peace talks, Mr Rose said "every day we're one day closer to the end of this".
"But every day the end of it seems further away and every day things just get worse in Gaza," he said.
"Today is worse than yesterday and tomorrow will be worse than today, that's just the reality of the situation as people are being ground down as more people are being killed," he added.
He called on "all sides on the international community and the parties to the conflict to deliver on these peace talks".
He said that while "they're not delivering, we insist upon the parties to the conflict to respect the inviolability of our premises and to allow the safe, unimpeded and sustained access to humanitarian assistance inside Gaza and around the Gaza Strip to meet the needs of the civilian population who are living in absolutely desperate conditions."
