New York Times

TEHRAN, June 18 - The accusation of voting irregularities came from Mehdi Karroubi, a cleric and former speaker of Parliament known as a conciliator, who said he would continue to press his case publicly unless the country's supreme religious leader ordered an independent investigation.

It was a bold move in a country that does not generally tolerate such forms of public dissent, and it threw an element of confusion and uncertainty into the race just as the authorities were finalizing the election results, planning for the runoff and pointing to the outcome as a validation of this country's religion-based system of government.

The Interior Ministry issued final figures Saturday night, saying the former two-term president, Ali Akbar Hashemi Rafsanjani, would face off against the hard-line mayor of Tehran, Mahmoud Ahmadinejad, in a runoff it said would probably be held next Friday. It was unclear what, if any, effect the accusations of fraud would have on the planned vote.

Mr. Ahmadinejad's strong showing came as a shock to the political establishment here. He had hovered at the back of the field of candidates in pre-election opinion surveys and his political base was said to be limited to the capital city. An element of the bizarre in the events on Saturday came as Mr. Ahmadinejad announced that he would be in the runoff hours before the ministry issued its own results.

The government did not immediately respond to the charges of vote tampering, but the cloud had been hanging over the race since the early morning hours when the Interior Ministry found its results being publicly contradicted on state television by the Guardian Council, the panel controlled by hard-line clerics that has the ultimate say over all government actions and often clashes with the reform-controlled elected government. The council has, for example, the power to unilaterally reject the outcome of the election.

Initially, the Interior Ministry had Mr. Rafsanjani first, Mr. Karroubi, the former speaker of the Parliament, in second, and Mr. Ahmadinejad third. Half an hour later the Guardian Council, which is not supposed to be involved in counting ballots, said Mr. Ahmadinejad was in first place.

Apparently hoping to head off an embarrassing public split, the departing president, Mohammad Khatami, visited the site where the ballots were being counted in the morning and offered words of assurance.

"All our efforts have been to hold a healthy election and to protect peoples votes," Mr. Khatami said in comments broadcast on national news. "I have come here to thank officials at the Interior Ministry and to make sure votes are being counted very carefully. If anyone has made any other comments, it is not right."

But the effort failed as Mr. Karroubi made his charges public. As the former speaker of Parliament, he was a member of the reform movement but often worked closely with the conservatives. He has made it clear that if he becomes president he will support working within the current system.

His charges gained some added currency on Saturday night when they were echoed by Dr. Mostafa Moin, the reform candidate who came in fifth after public opinion polls had shown him vying for second place. Dr. Moin said in a statement that military forces in the country joined together with some political organizations to rig the election and to promote a particular candidate, though he did not say which one.

"This is a warning for democracy," Dr. Moin said in the statement. "We must be aware that such efforts will eventually lead to militarizing the regime, and political and social supression. This is a threat for civil society and is blocking reform."

Mr. Karroubi accused the Guardian Council and elements of the Revolutionary Guard of working together to rig the election. He said the government of Mr. Khatami was powerless to change anything.

"There have been interferences, they have paid money," Mr. Karroubi said as he called on Ayatollah Ali Khamenei, the supreme religious leader, to set up an independent body to investigate the administration and outcome of the election.

In declaring himself a candidate in the runoff, Mr. Ahmadinejad dismissed Mr. Karroubi's charges as words from a sore loser.

"It is very obvious that the one who has lost would protest now," Mr. Ahmadinejad said. "I expect Mr. Karroubi, who is a cleric and wears sacred clothes, to make his comments with more attention."

When voters went to cast their ballots on Friday, public opinion polls, which are conducted by government controlled agencies, showed Mr. Rafsanjani in first place with Dr. Moin and the former police chief, Mohammad Baqer Qalibaf, competing for second. But the results confounded the expectations.

"It is very strange," Hermidas Davoud Bavand, a professor of international law at Alameh University in Tehran, said of the results. "As far as guesswork and assumptions and taking into consideration the popularity of the candidates, nobody predicted this."

Analysts trying to explain the candidates' come-from-nowhere successes said Mr. Ahmadinejad's candidacy seemed to represent the conservative movement's last stand in its effort to hold back a society moving toward more liberal ideas, while Mr. Karroubi's appeal was more pragmatic: he offered to give $60 a month to every Iranian if elected.

"Fifty or 60 dollars a month can make a big difference to a family with four or five kids," said Ahmad Zeidabadi, a political analyst in Tehran and a university professor. "These families figure if he keeps his promise, great, and if not, he is like the rest of them."

But others saw a dark hand in the election process. An aide to Dr. Moin said that their campaign had information that representatives of the Guardian Council who were only supposed to monitor polling places got involved in counting ballots. Mr. Karroubi was more specific in his charges, saying that money was paid in certain cities to encourage people to vote a certain way, and that the authorities pressured people to vote for the candidates supported by the hard-line religious leaders.

"I think some of the power bases have changed the decision," he said at his news conference. "I have documents. I can show tapes to prove there have been speeches to make people to vote for certain candidates."

The election controversy also served to underscore one of the most active fault lines in the Islamic republic, where elected government officials are on one side and appointed religious leaders on the other.

"The Guardian Council and the Interior Ministry represent two different powers," said Ramin Jahanbegloo, director of the Department of Contemporary Studies in the Cultural Research Bureau, a research institution based in Tehran. "It is a competition over controlling the statistics and controlling the status quo. The Guardian Council wants to control the status quo."

The Guardian Council also tried to inject itself into the calculation of how many voters turned out to the polls. Initially, the Interior Ministry said turnout was 55 percent. By 9 p.m., it reported that 29 million ballots were cast, with a turnout of about 62 percent - Mr. Rafsanjani came in first with 6.1 million votes, Mr. Ahmadinejad was second with 5.7 million and Mr. Karroubi was third with 5 million.

The Guardian Council announced Saturday morning a turnout of about 70 percent.

When asked by Iranian reporters on Saturday about the difference between the vote tally of the Guardian Council and the Interior Ministry, Mr. Khatami said: "Eventually they should be exactly the same. One or 2 percent is not important."

Nazila Fathi contributed reporting for this article.