An election worker counts votes at the the Independent Election Commission in Kabul , Afghanistan, on Sunday. (Rafiq Maqbool/Associated Press)

Charges of fraud in Afghanistan's presidential election are growing and they could sway the final result, the commission investigating complaints said Sunday.

The independent Electoral Complaints Commission had received 225 complaints since the start of Thursday's vote, including 35 allegations that are "material to the election results," said Grant Kippen, the head of the UN-backed body. The main complaints are over the rigging of ballot boxes, he added.

President Hamid Karzai's top challenger, former foreign minister Abdullah Abdullah, widened allegations of fraud against Karzai and his government on Sunday, saying ballots marked for Karzai were coming in from volatile southern districts where no vote was held, and that turnout was being reported as 40 per cent in areas where only 10 per cent of voters cast ballots.

"My focus today is on the big fraud. Big fraud, which can have an impact on the outcome of the election," said Abdullah. "This has to be prevented. That is critical for the survival of the process."

The U.S. special envoy to Afghanistan urged patience for the official complaints process to run its course before judging the vote's legitimacy.

"There are always rumours in Afghanistan," said Richard Holbrooke in the western city of Herat.

"We have disputed elections in the United States. There may be some questions. That would not surprise me at all. I expect it."

Millions of Afghans voted in the country's second-ever direct presidential election, although Taliban threats and attacks appeared to hold down the turnout, especially in the south.

Preliminary results are now expected on Tuesday. Final results won't be available until next month. If neither Karzai nor Abdullah wins 50 per cent or more, there will be a run-off vote, probably in October.