The conditional non-bailable arrest warrant was issued against the 70-year-old former president after he failed to turn up before the court for indictment.
"In view of the law governing the matter, the presence of the accused is required for proceeding with the case...Let a non-bailable warrant for production for the accused be issued for March 31, 2014 to be executed by the Inspector General of Police, Islamabad or any officer designated by him," said the order read out by Abdul Ghani Soomro, registrar of the court.
The court also directed the authorities to ensure fool-proof security arrangements on March 31 so that Musharraf, the first military ruler in Pakistan's history to face a treason trial, could be brought to the court.
The defence said they will challenge the order once they get a copy of it.
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"We will challenge the order once we get the order," Faisal Chaudhry, a lawyer for Musharraf told the media outside the 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 is facing treason charges for suspending and abrogating the constitution and imposing an emergency in November 2007.
This is the first time in Pakistan's history that a former military ruler has been put on trial for treason. If convicted,he could get life imprisonment or the death penalty.