Gates told reporters aboard his plane that a decision on strategy and troop levels might have to be taken before the outcome of disputed Afghan elections is fully resolved.

"My view is that whatever emerges in Kabul is going to be an evolutionary process," said Gates when asked about a possible run-off vote.

"The president will have to make his decisions in the context of that evolutionary process," he said.

Gates' comments appeared to diverge from White House chief of staff Rahm Emanuel, who suggested on Sunday that a troop decision would have to wait for a resolution of the disputed vote that could produce a "credible" government in Kabul.

The August presidential elections -- tainted by allegations of widespread fraud -- have caused serious concern in the Obama administration over the credibility of President Hamid Karzai's government and helped prompt a wide-ranging review of strategy.

Amid accusations of dithering from Republicans in Congress, Obama has been holding high-level meetings on the war in recent weeks and has held off making a decision on a request from the US commander in Afghanistan for tens of thousands additional forces.

Gates acknowledged the vote had "complicated" the situation in Afghanistan and it would take time for the political tensions to be settled.

The approach of winter meant the window for holding a run-off was closing fast, as snow would make it impossible for many Afghans to reach polling places, he said.

"I think the weather becomes a limiting factor in terms of the run-off," he said.

If there was a run-off in Afghanistan, Gates said he was confident the NATO-led force of more than 100,000 -- including nearly 68,000 American troops -- could provide security for the election along with Afghan security forces.

In the meantime, the United States and its allies would work to bolster the Kabul government's legitimacy and to stem corruption, he said.

"We are not just going to sit on our hands waiting for the outcome of this election and for the emergence of a government in Kabul.

"We have operations underway and we will continue to conduct those operations." he said.

In Kabul, a UN-backed watchdog overseeing Afghanistan's elections ordered votes from 210 polling stations thrown out Monday in a move that observers said deprived Karzai of an outright win.

The findings of the Electoral Complaints Commission (ECC) over the August 20 vote raised the prospect that Karzai could be forced into a second round or come under intense international pressure to stitch together a national unity government.

The Pentagon chief's press secretary, Geoff Morrell, said that Gates believed the Kabul government's legitimacy was not merely a matter of securing a clear outcome for the elections.

"For the secretary, the legitimacy question is beyond who's declared the victor in the elections," Morrell told reporters.

The question was "does this government, whoever's in charge, have the full faith and confidence of the Afghan people?"

Gates defended the pace of deliberations on Afghanistan and suggested Obama was moving closer to a decision.

"I think it's been a thorough process and I think we are now moving to the point where the president will begin to address specific options and then make his decision," he said.

With Secretary of State Hillary Clinton scheduled to travel next week and Gates on a tour of Asia this week, another round of White House strategy sessions on Afghanistan would have to wait until after next week, he said.

In Washington meanwhile Karzai's main election rival Abdullah Abdullah said he was open to either a run-off vote or other options to resolve Afghanistan's political paralysis.

The former foreign minister declined to elaborate on the other options amid speculation of a national unity government, after a UN-backed commission threw out more than one million fraudulent ballots from the August 20 election.

"While I am prepared to go for a run-off, at the same time the door is open," Abdullah, who accuses Karzai of rampant ballot fraud, told CNN.

Gates, who presided over a ceremony Monday in Hawaii for the new head of the US Pacific Command, was en route to Tokyo, where he will hold talks on Tuesday and Wednesday with the new government ahead of a visit next month by Obama.

The defense secretary was due in Seoul on Wednesday and Thursday before heading to Slovakia for a NATO summit on Friday expected to be dominated by the war in Afghanistan.

Gates, who in the past accused some European allies of falling short in their support for the Afghan mission, also said he was encouraged by the attitude of NATO members this year, saying they had shown a "renewed commitment" to the war effort.

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