UN schools in Gaza closed on Thursday as staff went on strike to protest the dismissal of workers' union chief Suheil al-Hindi.
The UN Relief and Works Committee took disciplinary action against al-Hindi "for breach of the Agency's rules and regulations," it said in a statement.
The union said in a statement that al-Hindi was fired for participating in functions attended by Hamas leaders.
Secretary of the union Yousef Hamdooneh announced the strike on Wednesday, and said that protests would escalate next week.
UNRWA expressed regret that 220,000 could not attend school on Thursday, noting in a statement that the strike would "jeopardize their eduction."
The agency said "proper and transparent mechanisms" existed to resolve staffing disputes.
"Strikes and the closing of UNRWA installations and preventing staff from providing services cannot and never will change staff disciplinary actions," UNRWA said.
"The decision to deny refugee children in Gaza education is even more shocking considering the level of trauma inflicted upon the children by war and blockade in the last few years," the agency added.