High drama was witnessed at the hearing as the court was due to indict Musharraf over his 2007 imposition of emergency rule.
One of Musharraf's lawyers Rana Ijaz was ordered out of the courtroom by Justice Faisal Arab, heading the three-man bench, after he called the judges "contract killers".
At the start of the hearing, Ahmed Raza Kasuri, another lawyer of Musharraf, presented a leaked secret letter written by an official of the interior ministry warning against a possible terror attack on the 70-year-old former army chief.
He said Musharraf will appear when the court summons him, however, the court will be responsible for any untoward incident with his client.
He said, "History will hold you (the court) responsible". Justice Arab countered that history itself would decide and asked the counsel not to cross professional limits.
Titled "Threat alert: 239", the letter claimed that TTP and al-Qaida fighters might target Musharraf.
"It seems that the terrorists have sympathisers in the security/cavalcade of Musharraf in order to assassinate him. The plan may materialise either using IEDs/VBIED or inside/outside the courts similar to the incident of (slain Punjab governor) Salman Taseer," stated the document.
Countering this argument, prosecutor Akram Sheikh expressed surprise that a secret letter was with the defence team even though the prosecution was not aware of it.
He said that Musharraf is a free man and the court should order that he be taken into custody so that security could be the government's responsibility.
He said the government will ensure three-tier security and that the number of personnel on duty to guard Musharraf would be doubled.
Currently about 1,200 security personnel are put on duty to ensure Musharraf's safe travel to the special court.
Kasuri had said on Monday that Musharraf will not appear in court.
"How can he appear before the court when the court itself is not safe," Kasuri had said.
Citing the leaked letter, he said Musharraf's life was under serious threat.
"The ministry of interior is the complainant in the case. This time we are not saying he is under threat. The complainant is saying so. The letter clearly says that he may be attacked on his way from the AFIC (Armed Forces Institute of Cardiology) to court," Kasuri said.
This is the first time in Pakistan's history that a former military chief is facing trial for treason.