A two-judge bench led by Justice Jawad S Khwaja issued the directives after hearing preliminary arguments on five petitions seeking Musharraf's trial for treason for subverting the constitution and declaring an emergency in 2007.
The bench said Musharraf or his lawyer should appear in court tomorrow to respond to the allegations.
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The bench also issued notices to the government, Musharraf and other respondents to respond to the petitions and adjourned the case till tomorrow.
The petitioners asked the apex court to direct the government to prosecute Musharraf under the High Treason (Punishment) Act of 1973.
"It is necessary to issue notice to the respondents in these petitions. The office shall ensure service of notice to the respondents for tomorrow," Justice Khwaja said.
The Interior Ministry should ensure that "the respondent (Musharraf) does not leave the jurisdiction of Pakistan", he said.
Most of the petitions against Musharraf have been filed by lawyers who want the former military strongman tried for treason for imposing emergency and deposing dozens of judges in 2007.
"Musharraf should be prosecuted for high treason because he is guilty of subverting the Constitution," lawyer Hamid Khan told the court.
"He should be punished with death or be jailed for life," Khan said.
The lawyers pointed out that the Senate or upper house of parliament had passed a resolution in January 2012 that said Musharraf should be arrested on his return but the government had not acted on it.
The lawyers further argued that the government had failed to act on an earlier Supreme Court order directing authorities to take action against Musharraf for violating the Constitution.
Justice Khwaja remarked that the apex court had already declared the emergency imposed by Musharraf in 2007 as unconstitutional and asked what action authorities had taken against him.
Justice Khilji Arif, the other member of the bench, said the Constitution states that those who violate it must be tried under Article 6, which relates to high treason.
Talking to reporters after the hearing, the lawyers for the petitioners said Musharraf should not be accorded "VIP protocol" as he is an accused in several cases.
They said the case against the former President in the Supreme Court would ensure that no one subverts the Constitution in future.
They said the generals and other persons who backed Musharraf too should be held accountable.
Hours before the hearing began this morning, Chief Justice Iftikhar Chaudhary withdrew himself from the three-judge bench that was formed last week to take up the petitions against Musharraf.
Chaudhry withdrew from the bench after questions were raised about his impartiality as he was one of the dozens of judges deposed by Musharraf.
The main petition by Taufiq Asif, a senior leader of the Rawalpindi High Court Bar Association, seeks Musharraf's trial for treason for imposing emergency.
On Friday, another petition was filed by Ahsanuddin Sheikh, a former president of the Lahore High Court Bar Association. The petitioners also asked the apex court to direct the government to take Musharraf into custody.
Musharraf returned to Pakistan last month after nearly four years of self-exile to lead his All Pakistan Muslim League party in the May 11 general election. He is currently in the federal capital.
The former dictator's nomination papers for three parliamentary seats in Karachi, Kasur and Islamabad have been rejected.
However, his papers for another seat in Chitral were accepted.
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