"WFP confirms that two WFP staff of Malaysian nationality have left DPR Korea and arrived in Beijing today," the UN agency said in a statement.
"The staff members are international civil servants and not representatives of their national government. They work on WFP's programmes in DPR Korea," it added.
North Korea and Malaysia Tuesday banned each other's citizens from leaving their countries, with Kuala Lumpur saying its nationals were effectively being held "hostage".
Malaysia's prime minister Najib Razak on Wednesday ruled out severing ties with North Korea and said his government would seek to negotiate to secure the release of Malaysian citizens in North Korea.
The Malaysian foreign ministry said 11 of its citizens were currently in North Korea - three embassy staff, six family members and two who work for the UN's World Food Programme.
In a statement posted in both Malay and English, Najib said on Facebook: "Two of our citizens under the UN World Food programme were allowed to leave Pyongyang. Stella Lim and Nyanaprakash Muniandy have both safely arrived in Beijing."
"They carry UN laissez-passer documents," he said.
Seoul has blamed Pyongyang for Kim's assassination, and Kuala Lumpur wants to question several North Koreans, although the only one it has arrested so far was released last week for lack of evidence.
An autopsy revealed that VX nerve agent, a substance so dangerous it is classed as a weapon of mass destruction by the UN, was used to kill Kim.
The diplomatic dispute erupted last month when police rejected North Korean diplomats' demands to hand over Kim's body.
Kuala Lumpur announced the expulsion of the North's ambassador over the weekend and Pyongyang retaliated in kind.
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