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 — later quashed by the authorities — that the commission could loosen its strict rules.