"Bassem Khoury has resigned to protest the Palestinian Authority's agreement not to discuss the Goldstone report," the official said on condition of anonymity.
The UN Human Rights Council on Friday delayed a vote on a damning report by former international prosecutor Richard Goldstone on alleged war crimes by Israel and the Palestinian Islamist movement Hamas during the Gaza war.
The move followed a request by Pakistan, on behalf of the several Arab, Muslim and African states that supported the report, to defer endorsement.
Earlier, the Palestinian delegation to the council had stopped pushing for the report's immediate consideration because of US pressure, according to media reports.
Khuri, a political independent, was a new face in the government formed by Western-backed Palestinian Prime Minister Salam Fayyad in May. The team does did not include any members of Hamas, which rules Gaza.
The Palestinian Authority's minister for Jerusalem affairs, Hatem Abdel Qader, resigned in July over what he said was the government's failure to aid residents in battling Israeli housing demolitions.