Musharraf was driven to the Rawalpindi-based court from his plush villa on the outskirts of Islamabad where he is under house arrest for charges dating back to his 9-year rule.
The former president appeared before Judge Chaudhry Habib-ur-Rehman for the first time since the Rawalpindi-based court began hearing the case in 2008.
His lawyer asked the judge to withdraw an order declaring Musharraf a fugitive and to lift a freeze on his bank accounts and assets.
The court, which is conducting hearings behind closed doors for security reasons, had declared Musharraf a "proclaimed offender" or fugitive and frozen his assets in 2011 after he failed to cooperate with sleuths investigating the assassination.
The former army chief's lawyer said these orders should be withdrawn as he was now appearing in the court.
Musharraf, 69, was accused of providing inadequate security to Bhutto after she returned to Pakistan from self-exile in late 2007. She was assassinated during a political rally in Rawalpindi on December 27, 2007.
The judge directed Musharraf to cooperate with investigators and adjourned the case till May 3.
Chief prosecutor Chaudhry Zulfiqar Ali of the Federal Investigation Agency told reporters that Musharraf had not cooperated with investigators.
"While he was on bail for a month, he did not join the investigation. Today was the first time he appeared in the court," he said.
Musharraf has been living at his farmhouse at Chak Shahzad, which was declared a "sub-jail" last week after he was remanded to judicial custody for a fortnight.
After the hearing, he was driven back to his farmhouse amidst tight security.
Outside the court, scores of lawyers scuffled with a group of Musharraf's supporters. The lawyers beat the former dictator's supporters with sticks and damaged several cars.
Footage on television showed both groups lobbing stones at each other on a street outside the court complex.
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