A three-member bench, headed by Justice Faisal Arab, is hearing the case relating to treason charges against the former president for imposition of emergency rule in 2007.
During the hearing, Justice Arab said the court wanted to be apprised of the nature and seriousness of the threat against Musharraf.
"He (Justice Arab) took the intel alert warning attacks against Musharraf seriously. He wanted to be briefed about the issue and has asked for the head of intelligence agency responsible for the alert to come tomorrow," a court source told PTI.
The hearing of the case was adjourned until tomorrow.
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Meanwhile, lawyer Rana Ijaz of the defence team representing Musharraf, 70, reached the court for the hearing but the security personnel prevented him from entering the court premises today.
Ijaz was barred from entering the court on a written order of Registrar Abdul Ghani Soomro in wake of his verbal attack on Justice Arab during the treason trial yesterday.
Justice Arab had asked security personnel to remove Ijaz from the courtroom after the lawyer said that he had received "life threats" and presumed that Justice Arab was behind them.
He said he was Musharraf's lawyer and he was being prevented from defending his client.
Musharraf is slated to appear before the special court on Friday and would be indicted.
The former army chief did not appear in court yesterday following a security alert issued by the interior ministry saying that he might be targeted by al-Qaeda or the Pakistani Taliban.
The ministry told the court that the alert was a copy of information received from intelligence officials.