A U.N.-backed commission ordered a partial recount from about 10 percent of the country's polling stations after allegations of widespread fraud in the vote, which was supposed to install a legitimate government to confront the growing Taliban threat.
However, vote-rigging allegations have plunged Afghanistan into an electoral crisis at a time when Taliban militants are expanding from their southern strongholds into the north and west of the country.
In a sign of the growing threat, hundreds of militants launched fierce attacks Saturday against two isolated outposts in Nuristan province, killing eight American soldiers in the biggest loss of U.S. life in a single battle in more than a year.
Afghan officials said U.S. and Afghan forces had sealed off an area Monday where the assailants were believed hiding.
In Kabul, election officials said the recount began Monday morning with ballots from 274 of the country's 3,498 polling stations. Ballots from another 84 locations were selected Monday and were expected in coming days, according to the deputy director of the election commission, Zekria Barakzai.
Barakzai said the count should take about three days to complete and that the commission would be able to announce the final results "by the end of next week."
Preliminary results released last month showed Karzai won the August balloting with 54.6 percent, enough to avoid a runoff with second place finisher Abdullah Abdullah. A recount could push down Karzai's numbers down below the 50 percent mark and force a runoff with Abdullah, a former foreign minister.
If a runoff were required, Barakzai said it must be held within two to three weeks of the announcement of the final results. Winter snows typically start in mid-November, making much of the country impassable.
Waiting for spring to hold the poll could create a power vacuum in a country already destabilized by the resurgent Taliban and delay both government projects and military operations.
Preliminary results took weeks longer than expected, and there have already been delays in the recount process. Election officials had previously said they would recount 313 of 3,063 suspect polling stations. Barakzai said they had misapplied the criteria for designating questionable ballot boxes and the higher number reflects the true count.
Whenever fraud is found among votes in one of the 358 sample boxes, all the votes in that box will be tossed. For votes in the remaining suspect boxes, the level of fraud in the sample will be used to decide what percentage of votes to void for each candidate.
Bolstering Afghanistan's weak and corruption-ridden government is considered key to President Barack Obama's strategy for curbing the Taliban insurgency so that U.S. and other international troops can go home.
However, fraud allegations threatened to undermine those plans at a time when the Taliban was proving to be a skillful and determined adversary.
The Obama administration is also divided over a request by the top military commander here, Gen. Stanley McChrystal, to send up to 40,000 more U.S. soldiers to Afghanistan. Obama is considering a range of ideas for changing course in Afghanistan, including scaling back, staying put or sending more troops to fight the insurgency.
U.S. officials also are waiting for the results of the Afghan elections, as disturbing reports of fraud grow.
As the debate rages in Washington, the NATO command reported that two more international soldiers, including one American, were killed in recent fighting. A statement from the alliance said a U.S. soldier died of wounds suffered in a bombing Sunday in southern Afghanistan.
The statement said a second service member died of wounds in a roadside bombing Monday, also in the south, but the victim's nationality was not released.
At least 16 U.S. service members have been killed in Afghanistan so far this month - matching the American death toll for all of October in 2008.
The latest deaths followed the fierce weekend assault against the Nuristan outposts, located about 20 miles (30 kilometers) from the border with Pakistan. About 20 Afghan security troopers were captured, officials said.
Nuristan Gov. Jamaludin Badar told The Associated Press that U.S. and Afghan forces had surrounded the assailants but there was no major fighting Monday.
The Taliban claimed responsibility for the attack. NATO spokesman Brig. Gen. Eric Tremblay said the assailants included a mix of "tribal militias," Taliban and fighters loyal to Sirajuddin Haqqani, an al-Qaida-linked militant based in sanctuaries in the tribal areas of Pakistan near the Afghan border.
McChrystal had planned to shift U.S. troops away from remote outposts that are difficult to defend and move them into more heavily populated areas as part of his new strategy to focus on protecting Afghan civilians.