Eide's reputation was under scrutiny after allegations from Peter Galbraith, his American deputy, 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.
Al Jazeera's Steve Chao, reporting from Kabul, said: "There's little question that Kai Eide has been the international fall guy for a lot of issues. He's been blamed roundly for not speaking out large enough on behalf of the UN in regards to the elections tainted by fraud."
"There is a deep mystery here ... Just two weeks ago, Kai Eide met with a number of journalists in Kabul and dismissed rumours of him choosing to leave Kabul.
"He said very clearly that he had the support of the Americans... and that he was here to stay for some time to come."
Eide said he has proposed ways to make the international community co-operate more effectively in providing civilian assistance to Afghanistan, but that more needed to be done.
Nato in Afghanistan needed someone to co-ordinate work with provincial reconstruction teams and more expertise was needed from key donor countries, Eide said.
Speaking from Kabul, Eide lamented that civilian work remained too "fragmented," too "ad hoc," and expressed hope that future work done by the international community will be sustainable when foreign assistance declines.