By Maria Golovnina
KABUL (Reuters) - A U.N. panel annulled ballots from dozens of polling stations in Afghanistan's presidential election on Thursday, kicking off a lengthy fraud investigation that could keep Afghans locked in political uncertainty for months.
The August 20 election has alarmed the West whose troops are involved in an increasingly unpopular military mission. President Hamid Karzai, on course to win in a single round unless the fraud watchdog overturns the outcome, has defended the vote as honest.
Preliminary results gave Karzai 54 percent of valid votes tallied this week -- enough to avoid a runoff with his closest rival, former foreign minister Abdullah Abdullah.
Western powers originally praised the ballot as a success in a country where the Taliban insurgency is now at its fiercest. However confidence in Karzai's handling of the vote has eroded as allegations of fraud have continued to mount.
An Electoral Complaints Commission (ECC), appointed mainly by the United Nations, can veto the tally and has said it has found evidence of fraud. It ordered a partial vote recount this week.
In a statement on Thursday, the ECC said it had already canceled all ballots at dozens of polling stations in Ghazni, Paktika and Kandahar provinces -- its first step in a complicated process that officials have said could last weeks, if not months.
"Investigation and subsequent decisions were taken in response to complaints received by the ECC during the polling and counting period," said the commission, run by a Canadian.
Most places included areas where pro-Karzai voting was particularly visible. In Paktika, one of the provinces, Karzai got 91.9 percent against Abdullah's 3.8 percent, according to preliminary partial results issued this week.
The ECC said it had found a number of "indicators of fraud" such as unfolded and miscounted ballots, votes for candidates inserted inside bundles for other candidates, and lists of voters with numerous fictitious card numbers.
It did not say how many votes it has invalidated in total so far. Based on preliminary results released with 91 percent of polling stations tallied, more than 400,000 ballots for Karzai would have to be annulled to require a second round.
Facing mounting diplomatic awkwardness over an election with disputed credibility, the West has distanced itself from the investigation but has expressed broad concerns.
"The European Union expects that all authorities and stakeholders will conscientiously respect the Electoral Law and refrain from pre-judging any result until it has been properly certified," said Sweden, which currently holds EU presidency.
"RECIPE FOR INSTABILITY"
These concerns have galvanized Abdullah and his supporters who have condemned the election as rigged.
"I'm not talking about just my own supporters, but those who cast their vote for Mr Karzai," Abdullah told BBC radio. "Their vote is now part of the fraud. And on top of that, a fraudulent outcome: illegitimate rule for another five years.
"I think this in itself is a recipe for instability in this country," he added.
Security and instability remain big concerns as a resurgent Taliban continue to gain strength across the country, including long-quiet and peaceful areas in northern Afghanistan.
A security map by policy research group the International Council on Security and Development has shown a deepening security crisis with substantial Taliban activity in at least 97 percent of the country.
Despite election allegations, Karzai has praised officials for carrying out the vote with "honesty and impartiality." Complete preliminary results are expected on Saturday, a spokesman for the election commission said.
The ECC has now ordered a recount from polling stations where one candidate received more than 95 percent of the vote or more votes were cast than the expected maximum of 600.
"Unless the 'clear and convincing evidence of fraud' found by the ECC is addressed, it will be impossible to determine the will of the Afghan people," the National Democratic Institute, a U.S. non-profit group which monitored the poll, said in a statement.
(Additional reporting by Jonathon Burch in KABUL, Paul Tait in SINGAPORE; Writing by Maria Golovnina; Editing by Nick Macfie)
(For more Reuters coverage of Afghanistan and Pakistan, see: http://www.reuters.com/news/globalcoverage/afghanistanpakistan) (Editing by Sugita Katyal)