The indictment by a three-member special bench constituted to conduct the trial makes Musharraf the first army chief to be tried for sedition in a country ruled by the military for more than half of its 67-year history. Prime Minister Nawaz Sharif needs the support of his defence forces to negotiate deals with Taliban militants and end more than a decade of violence.
"If the case goes on, definitely this will become a serious source of irritation for the military," said Hasan Askari Rizvi, a Lahore-based security analyst who previously taught at Columbia University in New York. "If these things continue, you will see problems in civil and military relations in the coming months."
Musharraf, 70, was brought to court with a police escort, pictures from Geo TV showed, after security agencies and his lawyers warned of threats to his life. He survived at least four assassination attempts by Islamic extremists while in power from 1999 to 2008.
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Ahmed Raza Khan Kasuri, a defence lawyer, said that Musharraf has pleaded non-guilty. The former army chief has also sought permission to visit his ailing mother in Dubai, he said.
Sharif, who gained power for a third time in May's election, was deposed by Musharraf in a 1999 coup after a dispute over an occupation of Indian-controlled territory in Kashmir. Soon after taking charge in June, Sharif said Musharraf would have to answer for his 2007 action.