Ahmadinejad's main challenger, moderate former Prime Minister Mir Hossein Mousavi, had nearly 29 percent of the votes cast, according to the commission which is part of the Interior Ministry.
Earlier Friday, Iran's IRNA news agency announced that Ahmadinejad was re-elected in a nationwide election after the polls closed Friday. The official count is still not ready, but supporters of the two front-runners, Ahmadinejad and Mousavi, have claimed victory.
Mousavi said at a Tehran press conference that he was the clear winner of the votes but accused the government of having made numerous legal violations.
Iranians packed polling stations from boutique-lined streets in north Tehran to conservative bastions in the countryside Friday with a choice that has left the nation divided and on edge: keeping hard-line President Ahmadinejad in power or electing a reformist who favors greater freedoms and improved ties with the United States.
Turnout was massive and could break records. Crowds formed quickly at many voting sites in areas considered both strongholds for Ahmadinejad and Mousavi, who served as Iran's prime minister in the 1980s and has become the surprise hero of a powerful youth-driven movement.
"I hope to defeat Ahmadinejad today," said Mahnaz Mottaghi, 23, after casting her ballot at a mosque in central Tehran.
Outside the same polling station, 29-year-old Abbas Rezai said he, his wife and his sister-in-law all voted for Ahmadinejad.
"We will have him as a president for another term, for sure," he said.
Voting was extended by six hours to midnight (1930 GMT, 3:30 p.m. EDT) to allow those still in line time to cast ballots.
Highly charged atmosphere, blistering recriminations
The fiery, month-long campaign unleashed passions and tensions. The mass rallies, polished campaign slogans, savvy Internet outreach and televised
debates more closely resembled Western elections than the scripted campaigns in most other Middle Eastern countries.
U.S. President Barack Obama said Iran's robust debate leading up to elections shows change is possible there, and it could boost U.S. efforts to engage Tehran's leadership.
In a sign of the bitterness from the campaign, the Interior Ministry - which oversees voting - said all rallies or political gatherings would be banned until after the announcement of results, expected Saturday.
In the only violent episode to be reported, a campaign organizer for Mousavi said about a dozen Ahmadinejad supporters attacked one of his campaign offices in Tehran with tear gas.
No one was injured, and police quickly dispersed the group, said Saeed Shariati, head of Mousavi's youth cyber campaign. There was no independent confirmation of the attack.
The cyber campaign ran several Web sites and Facebook pages supporting Mousavi. Authorities blocked at least three of them Friday.
The highly charged atmosphere brought blistering recriminations against Ahmadinejad - whom Mousavi said was moving Iran to a dictatorship - and a
stunning warning from the ruling establishment. The political chief of the powerful Revolutionary Guard warned Wednesday it would crush any revolution against the Islamic system by Mousavi's green movement - the signature color of his campaign.
The outcome will not sharply alter Iran's main policies or sway high-level decisions, such as possible talks with Washington. Those crucial policies are all directly controlled by the ruling clerics headed by the unelected Supreme Leader Ayatollah Ali Khamenei.
But Mousavi has offered hopes of more freedoms at home. If elected, he could try to end crackdowns on liberal media and bloggers and push for Iran to embrace Obama's offer of dialogue after a nearly 30-year diplomatic freeze. He favors talks with world powers over Iran's nuclear program, which the United States and others fear is aimed at making weapons. Iran says it only seeks reactors for electricity.
Iranians around the world also voted. In Dubai, home to an estimated 200,000 Iranians, the streets around the polling station at the Iranian consulate were jammed with voters overwhelmingly favoring Mousavi.
"He is our Obama," said Maliki Zadehamid, a 39-year-old exporter.
With the race too close to call, a top election official predicted turnout could surpass the nearly 80 percent in the election 12 years ago that brought President Mohammad Khatami to power and began the pro-reform movement.
A strong turnout could boost Mousavi. He is counting on under-30s, who account for about a third of Iran's 46.2 million eligible voters.
In Tehran's affluent northern districts - strongly backing Mousavi - voters waited for up to an hour to cast ballots. Mahdi Hosseini, a university student, blasted the firebrand Ahmadinejad for degrading Iran's image in the eyes of the world.
Ahmadinejad brought Iran international condemnation by repeatedly questioning the Holocaust.
In the conservative city of Qom, home to seminaries and shrines, hundreds of clerics and women dressed in long black robes waited to vote in a long line outside a mosque. Ahmadinejad's campaign has heavily courted his base of working-class families and tradition-minded voters with promises of more government aid and resistance to Western pressures over Iran's nuclear ambitions.
There were no reports of serious problems at the polls. But a top Mousavi aide, Ali Reza Beheshti, said some polling stations in northwestern and southern provinces ran out of ballots, claiming it was a deliberate attempt by the government to keep people from voting.
Iran's elections are considered generally fair, but the country does not allow international monitors. The ruling clerics, however, put their stamp on the elections from the very beginning by deciding who can run. More than 470 people sought to join the presidential race, but only Ahmadinejad and three rivals were cleared.
During the 2005 election, there were some allegations of vote rigging from losers, but the claims were never investigated.
After casting his vote in the white ballot box, the Supreme Leader Khamenei urged Iranians to remain calm.
"As far as I see and hear, passion and motivation is very high among people," Khamenei told reporters. "If some intend to create tension, this will harm people," he added.
After voting at a mosque on Friday in eastern Tehran, Ahmadinejad commented on the high turnout.
Interior Minister Sadeq Mahsouli said reports to election officials indicate an unprecedented turnout will be recorded in the country's election history, according to the official IRNA news agency.
Mousavi voted with his wife at a mosque in Tehran's southern outskirts.
In the southeastern city of Zahedan - where a bomb blamed on Sunni militants killed at least 25 people at a Shiite mosque last month - there were no reports of tensions. The bombed mosque was used as a polling station.
The race will go to a runoff on June 19 if no candidate receives a simple majority of more than 50 percent of the votes cast. Much depends on how many votes are siphoned off by the two other candidates: conservative former Revolutionary Guard commander Mohsen Rezaei and moderate former parliament speaker Mahdi Karroubi.
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