If upheld, the decision would reshape the electoral landscape by removing the most powerful and controversial candidates and leaving a field of moderates.
Disqualified candidates have 48 hours to appeal the decision, according to election rules. The final list of candidates will be announced on April 26. Thirteen others had their candidacy approved, including former Arab League chief Amr Moussa, moderate Islamist Abdel-Moneim Abolfotoh and former prime minister Ahmed Shafiq, according to Sultan.
A spokesman for el-Shater's campaign, Murad Mohammed Ali, called the decision "very dangerous" and said it gives a message that "there was no revolution in Egypt." Officials with all the campaigns vowed to appeal.
The struggle for power more than a year after Mubarak was ousted in a popular uprising has heated up with the approach of next month's presidential vote, in which Islamist hopes of capturing Egypt's highest post was recently challenged by the emergence of Mubarak's vice president Suleiman onto the political scene after a long disappearance from public view.
The Muslim Brotherhood, along with hard-line ultraconservative Salafis, captured more than 70 percent of the parliament seats in the first post-revolution elections.
Liberal and secular revolutionaries who spearheaded the mass protests that led to Mubarak's ouster have largely been sidelined.
The presidential election is due on May 23-24, with a possible runoff on June 16-17. The winner will be announced on June 21, less than two weeks before the July 1 deadline promised by the military rulers who took over after Mubarak to hand over power.
Saturday's announcement was the latest twist
The Muslim Brotherhood announced on March 31 that el-Shater would run for president, reversing an earlier pledge not to seek the office. The move came after weeks of complaints by the Brotherhood that the parliament they control is toothless and that the ruling military was blocking it from wielding power from parliament and preventing it from forming a government.
In what was seen as a countermove backed by the generals, Suleiman made an unexpected announcement a week later that he was entering the race for the presidential elections. Suleiman said he had decided to run to block Islamist rule and provide stability after more than a year of turmoil.
A judge close to the commission, who spoke on condition of anonymity because he wasn't authorized to disclose the information, said that Suleiman has not presented the proper number of endorsements. Each candidate needed at least 30,000 endorsements, including at least 1,000 from each of the country's 15 provinces, to join the race.
His campaign spokeswoman Reem Mamdouh said in an interview with the local CBC television network that they had not been officially notified about the decisions but would definite appeal.
"Suleiman will never withdraw and let down the hopes of the large constituency of Egyptians who supported him. This is not happening," she said.
Many observers also had been looking to the election commission for a decision about whether Abu-Ismail, a heavyweight candidate with the support of ultraconservative Salafis, would be disqualified over the question of whether his late mother had dual Egyptian-U.S. citizenship. A new election law passed after Mubarak's ouster bars an individual from running if the candidate, the candidate's spouse or parents hold any citizenship other than Egyptian.
The election commission had ordered the Interior Ministry to provide evidence showing whether his mother was officially documented in Egypt as having dual U.S. -Egyptian citizenship.
The Muslim Brotherhood fielded a back-up candidate last week, fearing that el-Shater would be disqualified on the grounds that he served time in prison in connection with his banned political activity under Mubarak. His lawyers say the ruling generals had dropped the charges.
On Friday, more than 10,000 Egyptians marched from mosques and protested in Cairo's Tahrir Square in a show of strength by Islamists demanding that Suleiman and other ousted regime officials be barred from running.
Ayman Nour, a liberal presidential hopeful, said the commission told him he was disqualified because of his imprisonment as a dissident under Mubarak's regime and because his name was not listed among registered voters.
He also promised to appeal, saying the decision was "politicized as the whole race is deeply politicized."