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Millions of Kenyans flooded into the polls on Monday and the voting itself went reasonably well, most observers said. But serious questions have begun to crop up in the tallying process, with unexplained delays in electronically transmitting the results from the polling places and public wrangling over which votes should be counted.

Election officials are counting the ballots by hand after abandoning the electronic tabulation system that has posted early returns, The Associated Press reported on Wednesday.

Given the deadly aftermath of Kenya's last major election in 2007, which was marred by vote rigging and then erupted in bloodshed, any electoral breakdowns or disputes could tear at the public's confidence in the vote, an outcome many people fear could set off violence again.

"I don't think the situation looks good," said Joel D. Barkan, a senior associate for the Africa program at the Center for Strategic and International Studies in Washington. "We are entering a quite potentially messy situation here."

Tensions were rising in the slums. Truckloads of soldiers in helmets and padded suits chugged through the streets, eyeing the crowds warily. Many shops remained closed, and Kenya's police inspector general promptly banned all demonstrations, saying Kenya had "no history" of peaceful protests.

As of Wednesday morning, about 60 percent of the votes had been tallied, giving a relatively large lead to Uhuru Kenyatta, the scion of one of the wealthiest, most powerful political families in Africa — 53 percent to 42 percent over Kenya's prime minister, Raila Odinga, who also traces his roots to one of the country's founding political dynasties.

But there was a wrinkle.

Kenyan election law says that the winning candidate must secure more than 50 percent of "all the votes cast" and late on Tuesday night, the election commission announced that it would include more than 300,000 rejected ballots as part of the total.

With the pool of votes suddenly enlarged, several analysts said that both candidates would receive a smaller percentage of the total and that Mr. Kenyatta might not clear the 50 percent threshold, forcing a runoff.

Ahmed Hassan, the head of Kenya's election commission, conceded that the number of ballots rejected for stray marks and other irregularities was "quite worrying," though election observers said it was not particularly surprising given the complexity of these elections. Voters had six ballots in their hands, for national and local races.

"We feel the Constitution is very clear," said Salim Lone, an adviser to Mr. Odinga. "The spoiled votes have to be included as part of the calculation."

Mr. Kenyatta's camp expressed displeasure with the decision, which may mean a protracted court battle after the preliminary results are announced, expected in the coming days. The risk, analysts said, is that Mr. Kenyatta's supporters might feel they were unfairly denied an outright victory.

Partial results showed that once again, Kenyans voted overwhelmingly along ethnic lines. Some areas voted 95 percent for the politician from their ethnic group, while other areas, equally poor, with people in very similar circumstances, voted 95 percent in the opposite direction.

"I guess we haven't come very far," said Maina Kiai, a prominent Kenyan human rights advocate. "We still use identity as the only factor in voting."

Enormous efforts were made this time around to move voters away from choices based on ethnicity and persuade them to consider other factors, like the candidate's résumé or policy proposals. The Kenyan news media, considered among the most independent and professional in Africa, even organized televised presidential debates, a first.

But in the end, the presidential candidates who tried to gain some momentum on issues-based campaigns, like Peter Kenneth and Martha Karua, got a minuscule share of the vote. It seemed that most voters still felt that the leader from their ethnic group was the best one to protect them — especially in an edgy environment where many fear a replay of postelection violence.

"The ethnic vote is often the one based on fear," Mr. Kiai said.

Kenya's ethnic arithmetic favors Mr. Kenyatta, who has been charged with crimes against humanity by the International Criminal Court. His ethnic group, the Kikuyu, is the country's largest, and along with the Meru and Embu, which often vote with it, they represent 22 percent of the population. He then chose William Ruto, a Kalenjin, to be his running mate, and the Kalenjin are the third-largest group in the country.

Mr. Odinga, a Luo, chose a Kamba running mate, Stephen Kalonzo Musyoka, but their combined numbers are far below the Kikuyu-Kalenjin alliance. Mr. Ruto has also been indicted on charges of crimes against humanity in connection with the election violence in 2007 and 2008.

Kisumu, a city in western Kenya and Mr. Odinga's ethnic stronghold, which exploded in riots in 2007 and 2008 during the last presidential election, was quiet on Tuesday.

"We're just waiting," said Christine Ololo Atieno, a seller of secondhand shoes and a passionate Odinga supporter. "People are still hoping that more votes will come in and things will change."

Mr. Odinga says he was cheated out of winning the last election, and many analysts say that Kisumu could explode again if there is vote rigging and Mr. Odinga loses again.