KABUL, Afghanistan — By early afternoon on Election Day for the president of Afghanistan, officials began to fret. At many polling stations, including some in the capital, Kabul, only the occasional voter had shown up. To allow for a bigger turnout, voting was extended by two hours.

The worry about low turnout has now turned into suspicion of artificially high turnout. Ballot boxes from several areas that had exceptionally high turnout in the Saturday election, surprising observers, have arrived at the Independent Election Commission’s tabulation centers brimming with votes. Some places of sparse voting reported turnout rates as high as 90 percent.

Despite evidence that the election was conducted more cleanly compared with years past, Afghans who braved Taliban violence to cast ballots now fear a muddled outcome because of fraud, dragging their war-ravaged country into a new crisis.

The fear amounts to a test for the Election Commission, which will declare the winner. It has vowed to discard bogus ballots and expressed confidence in detecting them with a new biometric voter identification system. But there was quickly talk that the commission could loosen its strict rules.

“The commission has the technical ability to address the fraud, so there is no worry about it,” said Mohammad Yusuf Rashid, the chief executive of the Free and Fair Election Forum of Afghanistan, a nongovernmental watchdog group. “But they should be honest in addressing the fraud.”

The campaigns of the two leading candidates, President Ashraf Ghani and his challenger, Abdullah Abdullah, both claimed they were in the lead even as the ballot counting had barely begun. Final results are not expected for more than a week.

The Election Commission was revamped ahead of the vote, with new commissioners appointed to replace predecessors jailed on charges of fraud and misuse.

Several commissioners expressed confidence in the biometric verification technology, which recorded each voter’s fingerprints and photograph at every polling station. The commissioners said their server computers, where the biometric data is stored, automatically separate duplicate votes.

The system is also designed so that every polling station could record a maximum of 400 votes. Some stations already are known to have reported more than 400 in what appear to be cases of sloppy fraud.

“We are obligated to only count the votes that are clean and have biometric verification,” said Mawlana Mohammed Abdullah, one of the commissioners.

Nonetheless, fears have grown that fraud could infect the outcome. The suspicion is driven partly by the patchy reporting of partial turnout data by the commission on the first day, and a jump in the turnout numbers of some provinces the following day.

In Spinboldak, a border district in the southern province of Kandahar, the number of voters was reported at more than 89,000 from a recently updated voter list of 103,000 that includes suspicious repeat numbers. The tally would constitute a nearly 90 percent turnout.

Supporters of Mr. Abdullah have said the Spinboldak numbers were hugely inflated and unrealistic. But several residents, reached by phone, said people had come out to vote in larger numbers.

“Everyone was heading for polling stations and I myself waited for 40 minutes at the polling site before my turn came,” said Haji Jumma Khan, an elder from Spinboldak. “I didn’t see any fraud. If it was committed, it must have been somewhere else.”

In Merzaka, a district in southeastern province of Paktia, the turnout was reported at about 80 percent. In some places in northern Faryab Province, where fighting discouraged most voters but turnout rates were high, ballot-box stuffing was the only possible explanation for the turnout.

“I am not going to lie, I didn’t see many people coming out to vote,” said Abdul Qayum Kohi, a local elder from Qaisar district, in Faryab. “There was fighting everywhere, mortars landing. Many people were too afraid to come out.”

Abdul Wahed Nasery, another elder from the district, said local strongmen had stuffed the boxes.

“They sat together, and each filled for their guy. They were saying, ‘We can’t leave these boxes empty,’” Mr. Nasery said. “We said, ‘But what about the biometric verification?’ They said, ‘Who is going to look?’”

After Kabul, the largest number of votes came from the eastern province of Nangarhar, with 255,000 votes. In addition to the Taliban threat, several of the province’s districts are intermittently threatened by members of the Islamic State, ensconced in the province’s Achin District. The provincial capital, Jalalabad, has been the target of frequent bombings.

Conversations with voters in several of the province’s districts suggested that while in some areas people voted in higher numbers than expected, in others concerns were high that ballot boxes had been stuffed late in the day.

One district in Nangarhar under particular scrutiny is Chaparhar, home of Fazlhadi Muslimyar, the speaker of the Senate and a campaigner for Mr. Ghani. On Tuesday, from his Senate seat, Mr. Muslimyar threatened the Election Commission’s chief, Hawa Alam Nuristani, who had said only biometrically verified votes would be counted.

“We will force even her daddy to count the non-biometric votes,” Mr. Muslimyar declared, in a televised speech.

Later in the day, Mr. Muslimyar apologized for his forceful language, but repeated his demand that even votes cast without biometric verification be counted.

Conversations with residents of Chaparhar suggested that turnout had been low on Election Day, suggesting Mr. Muslimyar had struggled to deliver votes for Mr. Ghani.

Local strongmen had arrived late in the day at the polling stations, creating chaos that may have included ballot stuffing, residents said, suggesting that Mr. Muslimyar was trying open a way for those votes to be counted as legitimate.

The discussion around changing the rules to include non-biometric votes has raised concern among several candidates, particularly Mr. Abdullah, who say that requirement is not open to debate.

“Not even one vote without biometric verification is acceptable to us,” said Rahmatullah Nabil, one of the candidates challenging Mr. Ghani.

Several election commission members said they were determined to expunge fraudulent votes, even if it shows an extraordinarily low voter turnout that creates the perception of an illegitimate election.

Officials have said the estimated total, 2.7 million, is already a record low, but that is compared to the artificially high numbers of earlier, fraud-riddled elections.

Mr. Ghani’s camp, despite reiterating its respect for the Election Commission’s rules, has signaled flexibility.

“We don’t want the fraudulent votes to be counted, no matter who it belongs to,” said Daud Sultanzoy, a senior member of Mr. Ghani’s campaign. “But votes of people should not be wasted.”

Zabihullah Ghazi contributed reporting from Jalalabad, and Taimoor Shah from Kandahar, Afghanistan.

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