The council approved only six candidates out of the 1,010 who registered to run.
The final list effectively barred reformers seeking democratic changes within the ruling Islamic establishment from the presidential race.
The move was made as ruling clerics seek to consolidate their power in the June 17 vote following the departure of reformist President Mohammad Khatami.
The approved candidates included powerful former president Ali Akbar Hashemi Rafsanjani, who moves frequently between the hard-line and more-moderate camps and was seen as a front-runner in the race.
A leader of the Islamic Iran Participation Front, Iran's largest reformist party, said his party will boycott the polls.
''We are warning the Guardian Council that we will not participate in the election if it doesn't reverse its decision," top party member Rajabali Mazrouei said.
Similar outrage occurred last year when the council, a constitutional watchdog that supervises the elections, disqualified more than 2,000 reformists from legislative elections, leading to a low turnout. Reformists denounced that vote as a ''historical fiasco."
The Guardian Council is controlled by hard-liners loyal to Iran's supreme leader, Ayatollah Ali Khamenei, who has the final say on all state
The council barred women from running for the office.
'Iran's experienced democracy since the revolution'
The other approved presidential candidates were former police chief Mohammad Bagher Qalibaf, former radio and television chief Ali Larijani, Mayor Mahmoud Ahmadinejad of Tehran, former parliamentary speaker Mahdi Karroubi, and former head of the elite Revolutionary Guards Mohsen Rezaei.
Former Culture Minister Mostafa Moin, the sole candidate of the Islamic Iran Participation Front, was among those disqualified.
Khatami, who came to power in a landslide in 1997, was regularly stifled in his attempts to bring political and social reforms by hard-line clerics led by Khamenei.
He is barred by law from seeking a third term.
Rezaei, Larijani, Ahmadinejad, and Qalibaf are widely seen as Khamenei candidates because of their loyalty to him. All of them are former military commanders.
Karroubi is a hard-liner-turned-reformer who has lost his popularity among the youth and reformists because of his increasing support of Khamenei and his hard-line policies.
With the reformist movement severely weakened, Rafsanjani is seen as the most credible force to stop hard-line allies of Iran's supreme leader from seizing the post of president.
But Rafsanjani has changed his loyalties frequently in the past, sometimes backing the hard-liner camp, sometimes taking a more moderate line and seeking to build ties with the West.