The mass-circulation JoongAng Ilbo, quoting an anonymous source familiar with North Korean affairs, said that Kung Sok-Ung had been removed from his post and expelled from Pyongyang to a rural farming area with his family.
It said the purge was ordered by supreme leader Kim Jong-Un following the defection of the North's deputy ambassador to Britain, Thae Yong-Ho, and his family to the South two months ago.
"Since Thae Yong-Ho's defection in late July, there has been an overall inspection throughout the foreign ministry," the source said.
The report said four other high-ranking diplomats in charge of European affairs were also expelled from Pyongyang.
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The 72-year-old Kung is a veteran diplomat who had been looking after North Korea's diplomacy with Russia and Europe for nearly two decades.
Since taking power in 2011, Kim has ordered numerous executions and purges of high-ranking officials to solidify his grip on power.
In August, South Korea's unification ministry confirmed that the North executed a vice premier for education for showing disrespect to the leader during a meeting.
South Korea's Yonhap news agency has put the number of party officials executed during Kim's rule at over 100.