A U.N. spokeswoman, Ishrat Rizvi, says staff members will either leave the country or be moved to safer areas in Pakistan.
News organizations quote Rizvi and a U.N. staffer in Pakistan as saying the relocation measures will last about six months.
At least 11 U.N. workers have been killed in Pakistan this year, including five in an October bombing at the U.N. World Food Program headquarters in Islamabad.
In other news, Pakistani security officials say a suspected U.S. drone strike has killed at least two people in North Waziristan, a tribal region near the country's border with Afghanistan.
Reuters news agency says missiles hit a home where militants were believed to be hiding.
In South Waziristan, Pakistani security forces have raided a hospital used by militants, killing at least four foreign fighters.
Officials said Pakistani forces also arrested more than 20 suspected militants in Wana, the main town in the region that is a stronghold of the Pakistani Taliban.
On Wednesday, a spokesman for Taliban's main faction in Pakistan, Tehrik-e-Taliban Pakistan commander Asmatullah Shaheen, claimed responsibility for Monday's attack on a Shi'ite religious procession the southern city of Karachi that killed 44 people. He also warned of more attacks in the coming days.
But on Thursday, another Taliban spokesman, Azam Tariq, denied the group is responsible.
In a separate development, Pakistani officials said they had arrested the senior Taliban leader in Punjab province. Police said Khalil Ullah was the mastermind of a bombing at a busy market earlier this month (December 7) in the provincial capital of Lahore that killed at least 48 people.
The Pakistani military has been carrying out a campaign against the Pakistani Taliban in South Waziristan. Militants have retaliated with bombings and shootings across the country.
Military officials say Pakistani security forces killed four alleged militants during a "search and clearance operation" near the Barikot region of South Waziristan. In a Thursday statement, the military also said one soldier was killed after militants opened fired on security forces at a checkpoint in the region.