"Non-bailable arrest warrant has been issued which will be implemented on March 31 in case he fails to appear before the court," Abdul Ghani Soomro, Registrar of the special court announced.
The defence said they will challenge the order once they get a copy of it.
"We will challenge the order once we get the order," Faisal Chaudhry, a lawyer for 70-year-old Musharraf told the media outside the special court.
The special court had earlier in the day reserved its judgement till afternoon.
The defence had claimed that Musharraf cannot appear due to security concerns.
A three-member bench, headed by Justice Faisal Arab of the Sindh High Court, had summoned Musharraf today for him to be indicted.
Musharraf's counsel, Anwar Mansoor, submitted an application in the court requesting for his exemption.
He said the background checks need to be conducted on the security personnel deployed for Musharraf's security and this would take at least 6 weeks.
The judge noted that in case he does not appear, charges will be read out to the lawyer.
"It would be very difficult to present Musharraf before the court due to security concerns. The security alert says that he could be targeted like slain Punjab Governor Salman Taseer by his own bodyguards. So as per protocol each of the 1,600 security personnel have to be screened and it will take few weeks," Kasuri told reporters.
He also claimed that the government and the army were not on the same page on the issue of Musharraf's trial. Kasuri accused Prime Minister Nawaz Sharif of vendetta politics.
This is the first time in Pakistan's history that a former military ruler is facing trial.
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