Maariv reported John Ging, the director of United Nations Relief and Works Agency for Palestine Refugees in the Near East, was forced to flee after refusing to cooperate with Hamas.
U.N. spokesman Farhan Haq told the daily U.N. press briefing Ging did not "flee."
"The Hamas de facto government has no influence whatsoever on who receives assistance from UNRWA and it has respected the independence of UNRWA," Haq said.
Days after Ging's departure, Hamas warned in a local newspaper anyone failing to comply with Hamas' instructions should leave Gaza, the official said.
Maariv said Hamas, which uses violence against organizations that are unwilling to cooperate, wants to clear all humanitarian assistance. The official said approximately $20 million in aid is sent to Gaza each month.
Israel's security establishment has expressed growing concern and a document compiled by the Defense Ministry outlines attempts by Hamas to steal funds allocated for humanitarian assistance, Maariv said.
The document, distributed to the Finance Ministry, Foreign Ministry, Israeli intelligence and organizations in the United States, warned funds allocated to rebuild Gaza following Operation Cast Lead could fall into the hands of Hamas.
The official said Hamas has already taken control of millions transferred by the Palestinian Authority to rebuild Gaza.