Musharraf was re-arrested in the Lal Masjid (red mosque) killing case after his lawyer deposited two bail bonds of one million rupees each in the Supreme Court Thursday, the Dawn reported.
Musharraf has already got bail in two cases, including the 2007 assassination of former prime minister Benazir Bhutto.
The court Wednesday granted bail to Musharraf with the judges observing that substantial evidence was not available to implicate the former president in the criminal conspiracy regarding Nawab Akbar Bugti's murder during a military operation in 2006.
Musharraf's lawyers said Wednesday that he was cleared to leave the country.
"We have put Gen. (retd.) Musharraf under house arrest in a case involving a military operation on an Islamabad mosque," Muhammad Rizwan, a senior official of the Islamabad police told reporters after Musharraf's arrest Thursday.
"We will present him before a court on Friday," Rizwan added, after visiting Musharraf's plush villa at the edge of Islamabad, which has been declared a sub jail.
A complaint against Musharraf in the Lal Masjid case was registered last month on the orders of a judge.