Pakistan's former ruler Pervez Musharraf has been re-arrested over a deadly commando operation at a mosque in 2007, a day after getting bail in another case.

The former Pakistani president is accused of being personally responsible for the deaths of more than 100 people after he ordered commandos to storm the Red Mosque in the capital, Islamabad.

A complaint against Musharraf in the Red Mosque case was registered two weeks ago on the orders of a judge.

The operation followed a week-long standoff between the mosque's supporters and security forces.

He had been granted bail in three other cases, including one relating to the assassination of former Prime Minister Benazir Bhutto.

His lawyer said on Wednesday that the former army ruler was cleared to leave the country after a three-member Supreme Court bench granted bail to the former president over death of Akbar Bugti, the main rebel leader in the southwestern province of Balochistan.

Bugti was killed during an army operation in 2006 when Musharraf was head of the state.

As well as the Bugti and Bhutto cases, Musharraf also faces cases over the suspension of judges during emergency rule, which he imposed in 2007.

Musharraf was forced out of office after trying and failing to fire the country's chief justice.

The Taliban have threatened to kill the 70-year-old former general, who as president allied Pakistan with Washington in the US "war on terror" in the wake of the 9/11 attacks.

The former president and head of the army went into exile in 2008, but returned earlier this year to participate in the general elections, but he was barred from standing in the election, won convincingly by Prime Minister Nawaz Sharif - the man he ousted from power in 1999.