Musharraf is accused of conspiracy to murder Benazir Bhutto, who died in a gun and suicide attack in December 2007. It is one of three cases he is fighting in the courts since returning home last month after four years in self-imposed exile.
His arrest and disqualification from contesting elections on May 11 have been a humiliating blow for the former chief of Pakistan.
Despite a heavy police and paramilitary presence, scuffles broke out between lawyers and Musharraf supporters, who threw stones and beat each other with sticks outside the court building, an AFP reporter said.