Kai Eide, a Norwegian diplomat, said he is not stepping down but has asked U.N. Secretary-General Ban Ki-Moon to start searching for a replacement.
"I'm not resigning," Eide told The Associated Press in a telephone interview. "It's a question of telling New York that I'm not renewing my contract."
Eide's tenure was tarnished by allegations from his American deputy, Peter Galbraith, that he was not bullish enough in curbing fraud in the August presidential election. Eide denied the charge and said controversy over the election was not linked to his decision not to renew his contract.
"The election controversy was between Peter Galbraith and the rest of the international community," he said, adding his plan when he took the job was to stay two years, as did his predecessors.
"Kai Eide is sticking to the timetable that he outlined when he took the job in March 2008," Dan McNorton, a U.N. spokesman in Kabul said.
Eide said he has proposed ways to make the international community cooperate more effectively in providing civilian assistance to Afghanistan but more needs to be done. NATO, which oversees military operations in Afghanistan, needs someone to coordinate work with provincial reconstruction teams and more expertise is needed from key donor countries, Eide said.
Speaking in Kabul where he said he was writing a paper, Eide lamented that civilian work remains too "fragmented," too "ad hoc," and expressed hope that future work done by the international community will be sustainable when foreign assistance declines.
He said he planned to stay until his contract expires but he wanted to give U.N. headquarters time to find someone to fill the job.
"I don't want there to be a vacuum," he said.