Judge Chaudhry Habib-ur-Rehman of the anti-terrorism court in Rawalpindi accepted a request from Balochistan Police to include Musharraf in the probe into Bugti's death.
Musharraf was the army chief when the operation against Bugti was ordered.
Shortly after the court issued the order, a five-member team of Balochistan Police went to Musharraf's farmhouse, declared a sub-jail by authorities, to question him.
Musharraf is facing charges over the death of Bugti.
A court in Balochistan had issued a warrant for his arrest over the killing in 2011.
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Sherpao asked the court to excuse him from personal appearances in future hearings for security reasons.
The court adjourned the matter till May 16.
Musharraf, 69, has been held at his farmhouse on the outskirts of Islamabad since he was arrested over the sacking of judges during the 2007 emergency and the assassination of former premier Benazir Bhutto.
He has been accused of providing inadequate security to Bhutto after she returned to Pakistan from self-exile in 2007.
Musharraf returned to Pakistan last month after nearly four years in self-exile to make a political comeback but he has been dragged to court over several issues.
On April 30, the Peshawar High Court banned Musharraf from contesting elections for the rest of his life.