Afghan voters filed more than 2,500 complaints of ballot box stuffing and other election irregularities, an official said Tuesday, as fraud allegations by the two candidates and their supporters threaten to provoke a new political crisis.

The campaign tone has been sharply more accusatory than that of the first round of voting on April 5, when Afghans had eight candidates to choose from and all promised to adhere to the results released by the Independent Electoral Commission.

The stakes are higher now that the field is narrowed to two men who are vying to replace Hamid Karzai and lead the country as most U.S. and allied forces withdraw by the end of 2014 and international aid diminishes. The prospect of a nasty fight over the results also could dampen hopes that the country will be able to hold its first-ever peaceful transfer of authority.

The Obama administration is watching carefully. Both presidential hopefuls -- Abdullah Abdullah and Ashraf Ghani Ahmadzai -- have promised to sign a security pact with the U.S. that will allow up to 14,000 American and NATO troops to remain in the country next year to advise the Afghan security forces and conduct counterterrorism missions. But they need to be inaugurated first.

Marine Gen. Joseph Dunford, the top U.S. military commander in Afghanistan, said Tuesday that the U.S. fully expects the deal to be signed and said he did not believe that the rapid deterioration of security in Iraq would occur in Afghanistan once U.S. combat troops leave. The U.S. left Iraq after the government in Baghdad refused to agree on a security arrangement.

He expressed confidence in the Afghan security forces, saying they performed extraordinarily well in providing security for the election, and now must maintain that momentum as the ballots and election materials are collected.

"Now we're into the difficult time of counting up the ballots and going through the complaint process," said Dunford. "The next several weeks will be important."

The first initial results are not due until July 2, then final results on July 22, according to the official timetable. But Abdullah Abdullah's team has questioned what it has determined is a 1 million vote lead by Ahmadzai in the early tallies. Abdullah pointed out it is a dramatic increase from the first round that put him in the lead with 45 percent of the vote compared to 31.6 percent for his rival.

"In which part of the country did the situation change so dramatically that the people changed their minds and then came and cast their votes?" he asked rhetorically Monday during a briefing with reporters in Kabul.

He also questioned the initial turnout estimate of 7 million, which would be 60 percent of the 12 million eligible voters and equivalent to the first round.

Ahmadzai's supporters dismissed the allegations and urged all sides to await the official results.  A spokesman said the 64-year-old former World Bank official had moved into the lead by better campaigning that focused on winning the support of the people, not just former rivals.

"There is a big difference right now, there is a difference of more than 1 million votes between our team and their team and that is why that they have started some conspiracies," said his spokesman Hamidullah Farooqi. Farooqi said there was fraud on both sides despite efforts to prevent it but urged patience.

"Despite all the problems, we are ready to accept the result and we also want other to keep their patience and accept whatever comes at the end," he said Tuesday in a telephone interview.

Nadir Mohsini, spokesman for the Electoral Complaint Commission, said his panel had received 2,558 complaints about the election by a midnight deadline to file them. "The majority of the complaints we have registered are from the election commission employees as well as the government officials," Mohsini said.

During the first round of the election, the commission reported receiving around 2,000 complaints, focusing on election workers and government employees who allegedly intervened in the process.

Observer groups said Saturday's vote was relatively smooth, although both candidates and observers said they had evidence of fraud ranging from ballot box stuffing to proxy voting. Several polling stations also opened late or failed to open at all because of security concerns, and many voters complained of ballot shortages.

Karzai, the only president Afghanistan has known since the fall of the Taliban following the U.S.-led 2001 invasion, was constitutionally barred from seeking a third term.

Abdul Khaliq Hussaini Pashai, a former member of the Independent Election Commission, said those investigating fraud must provide solid proof of their decisions before eliminating votes.

"If either candidate refuses to trust or accept the system as well as the commissions, this country will face a crisis, we should not let that happen," he said. "We hope for the sake of the nation that both teams accept the result and do not let this country suffer or face another crisis."