Pervez Musharraf, who ruled Pakistan between 1999 and 2007, was arrested on Friday.
The High Court ruled that the allegations amounted to an act of terrorism and ordered him to appear at Islamabad’s anti-terror court.
Pervez Musharraf has described the case against him as politically motivated.
Last month Pervez Musharraf returned from years of self-imposed exile hoping to lead his All Pakistan Muslim League (APML) party into the general election next month.
However, the former prersident has so far failed in his bid to register as a candidate with election officials.
Pervez Musharraf’s lawyers said it was unclear whether he would be detained under house arrest, in policy custody, or in jail.
APML spokesman Muhammad Amjad said Pervez Musharraf would fight the allegations in a higher court.
Judges are determined to prosecute Pervez Musharraf over his decision to dismiss judges including Chief Justice Mohammad Iftikhar Chaudhry.
Pervez Musharraf is accused of keeping the judges under house arrest for about six months in 2007 after he imposed emergency rule.
The former leader was brought to the court under heavy security.
Angry lawyers reportedly shouted slogans calling for Pervez Musharraf to be tried for treason.
His supporters and opponents clashed inside and outside the court.
Pervez Musharraf faces several other criminal cases and had been trying to stave off arrest since he returned.
The Pakistani Taliban have also vowed to assassinate former president Pervez Musharraf, who seized power in a 1999 coup.
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