The employees, who were joined by supporters on Monday, said they were protesting against a decision made last month by UNRWA to stop paying teachers for their annual leave days due to the financial hardship the agency is facing.
The protesters also demonstrated against UNRWA's decision to raise the number of students in each classroom to 50 per teacher, which they say will harm the quality of teaching and learning and leave many teachers unemployed.
However, Sami Mshasha, an UNRWA spokesperson in Jerusalem, said the demands of the protesters had already been met.
Mshasha said that the agency sent letters to 30,000 employees on Sunday, cancelling the unpaid leave proposal.
He also said that the possibility of raising the number of students to 50 was considered by UNRWA due to financial trouble, but added that eventually the number of students in each class will not exceed 41 students.
Emergency programmes threatened
Despite its financial hardships, UNRWA opened its 245 schools in Gaza as scheduled on Monday but many classrooms remained empty in light of the protests.
The agency announced earlier in August that it only had funding until the end of this month, when the school year was due to start in the Palestinian territories and Jordan.
It raised the possibility of laying off some of its staff for a year due to a lack of contributions from international donors.
New financial support allowed UNRWA to freeze those plans, but its employees were demanding that they be dropped entirely.
UNRWA, which began its operations in 1950, provides assistance and protection for about five million registered Palestine refugees in besieged Gaza, the occupied West Bank and Jordan, as well as in Lebanon and Syria.
The agency had said it required $100m to begin the 2015-2016 academic year in about 700 UN-run schools for half-a-million students across the Middle East.
Source: Al Jazeera