The court in Rawalpindi had said at the last hearing that Musharraf should be produced for today's hearing but he was not presented before the judge for security reasons, said chief prosecutor Chaudhry Zulfiqar Ali of the Federal Investigation Agency.
Though Musharraf was remanded to judicial custody for 14 days, the 69-year-old former military strongman will be held at his plush farmhouse at Chak Shahzad on the outskirts of Islamabad, which has been declared a "sub-jail".
The anti-terrorism court adjourned the case till May 14.
At the last hearing on April 26, Musharraf had been remanded to the physical custody of the FIA for four days so that he could be questioned by investigators probing Bhutto s assassination.
Referring to the FIA's decision not to produce Musharraf in court today, chief prosecutor Ali told reporters that the Interior Ministry has issued an order which said that the former President "faces the highest level of security threat".
"Due to this very reason, he was not presented in court but he was sent on judicial remand," he said.
The FIA's joint investigation team had completed its investigation against Musharraf and gathered "solid evidence" that "directly connects the accused with the commission of the offences with which he has been charged", Ali said.
"Musharraf has tried to shift liability and responsibility on others but there is solid evidence which proves he is guilty," he said.