Gates told reporters traveling with him to Asia that President Obama will have to make his decisions in the context of "evolving" issues.
The remarks come as Afghanistan's election commission in the disputed presidential poll after a fraud investigation dropped incumbent Hamid Karzai's votes below 50 percent of the total. Karzai accepted the finding and agreed to a second round vote.
The White House welcomed Karzai's agreement. Karzai, who was under heavy U.S. pressure to accept the U.N. findings, was "ensuring a credible process for the Afghan people which results in a government that reflects their will," President Obama said in a statement.
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"President Karzai's constructive actions established an important precedent for Afghanistan's new democracy," Mr. Obama said. "The Afghan Constitution and laws are strengthened by President Karzai's decision, which is in the best interests of the Afghan people. "
But while an election resolution is desirable, the decision on troop levels looms over the White House.
"A new election in Afghanistan will not make President Obama's decision about whether or not to increase troop strength significantly easier," said CBS News foreign affairs analyst Pamela Falk, "but it goes a long way to restore credibility to the oversight and decrease the view of corruption in the current government."
At the White House Tuesday, press secretary Robert Gibbs said it has not yet been determined whether Mr. Obama will wait to announce an Afghan strategy until after the results of the runoff. Gibbs told reporters he still expects that announcement to be made in "the coming weeks."
Regardless of the election's outcome, Gibbs said, "We've got to make sure we're making progress with a partner in that government." He also said the next U.S. strategy meeting on Afghanistan may be pushed back until early next week because Gates is traveling.
Among those most closely involved in seeking a resolution of the crisis is Sen. John Kerry, a Democrat and chairman of the Senate Foreign Relations Committee. He said in interviews over the weekend from Kabul that the election process had to be settled before the Obama administration could make a reasoned decision about whether to send additional troops and to commit other resources to stabilizing Afghanistan.
Kerry as at Karzai's side when the announcement was made in Kabul. He had met with Karzai on four occasions before the announcement.
As for the logistical challenges presented by the runoff, Secretary of State Hillary Rodham Clinton said Monday that a new vote was feasible within weeks, or that Karzai might try to negotiate a power-sharing arrangement with former Foreign Minister Abdullah Abdullah, who finished second in the August balloting.