The court in Rawalpindi had said 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 on Tuesday, 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.
Musharraf returned to Pakistan on March 24 after a nearly four-year long self-imposed exile abroad to contest the May 11 general elections. However, Pakistani authorities disqualified him from contesting the election, effectively putting an end to his ambitions for a political comeback.
As the investigation had been completed, there was no need for the FIA to seek an extension in Musharraf's physical custody.
Bhutto was assassinated by a suicide bomber after addressing an election rally in Rawalpindi in December 2007.
Musharraf was formally arrested by the FIA on April 25 after the anti-terrorism court directed investigators to include him in the probe into the assassination. He has been accused of failing to provide adequate security to Bhutto after she returned to Pakistan from self-exile.
He was also declared a fugitive by the anti-terrorism court after he refused to cooperate with the investigators. He is facing several other criminal cases.
Lawyers have petitioned the Supreme Court to put him on trial for treason for imposing emergency rule in 2007. He is also facing charges over the killing of Baloch leader Akbar Bugti in a 2006 military operation.
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