The court in Rawalpindi, before adjourning until May 3, issued the order Tuesday against Musharraf, who is already under a two-week house arrest at his sprawling villa outside Islamabad over a case relating to detention of Pakistani judges in 2007 when he was in power.
Musharraf was driven to the anti-terrorism court by authorities.
Benazir Bhutto, a former prime minister and wife of the current Pakistani president, died in a gun and suicide attack Dec. 27, 2007, in Rawalpindi, where she had earlier addressed an election rally. The Bhutto assassination has been under investigation since then.
Musharraf, 69, had previously been accused of failing to provide adequate security to Bhutto at her election rally appearance.
Dawn newspaper said Musharraf's appearance in the anti-terrorism court was his first over the Bhutto probe.
The report said there were scuffles between lawyers and Musharraf supporters after the court's order. The retired general was later driven back to his villa.
Among his other legal hurdles, Musharraf, who ruled the country for nine years after a coup in 1999, is also accused of treason stemming from the 2007 suspension of the constitution, imposition of emergency rule and detention of a number of judges.
However, earlier this week, a caretaker government, which has been put in place ahead of Pakistan's general elections next month, said it would leave the decision on the filing of any treason charges to the next elected government as the issue is beyond its mandate.
Musharraf returned to Pakistan last month after four years of self-imposed exile in London and Dubai to contest in the elections. However, the elections commission has turned down all his candidacy applications.
Musharraf and his attorneys have denied all the accusations, saying they are politically motivated.
Even since becoming an independent country in 1947, Pakistan has been intermittently under the rule of its powerful military for decades. Next month's elections, however, would mark the first time of a civilian government transition.
The Musharraf case is the first time a former military rule has come under such legal pressure.