Chaudhry also called for the suspension of the city's deputy administration chief and another senior police officer during a supreme court hearing to investigate the police response to the protest.
"The three officials have been suspended on the orders of supreme court of Pakistan," Brigadier Javed Cheema, an interior ministry spokesman, said.Casualties
The clashes on Saturday occurred outside the country's election commission and near the supreme court after Musharraf's candidature for another five-year term in power was approved.
Hospital officials told the court that Islamabad's hospitals treated 83 people, many for head injuries, after the violence. Casualties included 13 police officials, 31 journalists and two opposition politicians, state-run media said.
"We are extremely thankful to the chief justice," Mazhar Abbas, a senior official from the Pakistan Federal Union of Journalists, said after the supreme court hearing.
Kamal Shah, interior minister, told the court that the government had ordered an inquiry into the clashes.
On Friday, the court had dismissed opposition petitions against Musharraf's eligibility, ruling that he could contest the vote while continuing in his role as chief of the army.
Chaudhry, who was reinstated as the country's most senior judge in July after mass protests against his dismissal, was not on the nine-judge bench that heard the case.
"Pakistan needs a military leader who can control both civil and possible military extremism"
Creative_person01, Islamabad, Pakistan
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Musharraf, who seized power in a coup eight years ago, has said he will quit his military role before November 15 if he wins the presidential vote on October 6.
Last week, Chaudhry ordered the release of more than 100 detained opposition leaders and criticised Islamabad authorities for blockading the city with trucks and buses when Musharraf filed his election nomination papers.
Meanwhile, lawyers' groups planned strikes across Pakistan on Monday, and commentators have been predicting a volatile period leading up to the presidential election.