"This is a UN area and this constitutes, at the very least, a violation of the 1946 UN Convention," UNRWA deputy director Natalie Boucly told AP.
The case is currently being investigated by the UN Justice Department in New York.
Israeli bulldozers demolished parts of the UN agency's headquarters at the site in January.
This weekend, the country's government announced that it had approved the construction of facilities for the Ministry of Defense there. Defense Minister Israel Katz described it as a decision for "sovereignty, Zionism and security."
Israel has accused UNRWA of having a large number of employees with links to Hamas, a claim denied by the UN agency.
