A team of Balochistan Police arrested the former military ruler and grilled him for nearly four hours at his farmhouse on the outskirts of Islamabad, which was declared a "sub-jail" by authorities.
The five-member police team confirmed to reporters outside the sprawling farmhouse that Musharraf had been arrested over the killing of Bugti.
Musharraf, 69, was the army chief when the operation against Bugti was ordered.
Earlier in the day, Judge Chaudhry Habib-ur-Rehman of an anti-terrorism court in Rawalpindi accepted a request from Balochistan Police to include Musharraf in the probe into Bugti's death.
Shortly after the judge issued the order, the police team went to Musharraf's farmhouse to question him. Musharraf is facing charges over the death of Bugti.
A court in Balochistan had issued a warrant for his arrest in 2011.
Since his return to Pakistan in March after nearly four years in self-exile , Musharraf was first arrested on April 19 for detaining more than 60 judges during the 2007 emergency. He was again arrested on April 25 over the assassination of former premier Benazir Bhutto in 2007.
In a related development, Aftab Ahmed Khan Sherpao, who was Interior Minister in Musharraf's regime, appeared in an anti-terrorism court in Quetta for the hearing of a case over Bugti's killing.
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 is being held at his farmhouse due to threats to his life from the banned Tehrik-e-Taliban Pakistan and other militant groups. He has been accused of providing inadequate security to Bhutto after she returned to Pakistan from self-exile in 2007.
Lawyers have also petitioned the Supreme Court to put him on trial for treason for imposing emergency. Musharraf returned to Pakistan 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.