A Pakistani court on Friday ordered former president Pervez Musharraf to be detained for 14 days for the 2007 commando operation against a militant mosque.
The order was made hours after the court rejected a petition seeking to put the former president on the Exit Control List, which would prevent him from leaving the country.
Pakistan arrested Musharraf Thursday, a day after he was granted bail in the last major case against him, raising the possibility he could leave the country.
In the latest charge, Musharraf is accused of ordering a raid against an Islamabad mosque in 2007 to crack down on armed militants. The operation left a cleric and dozens of other people dead.
A complaint against Musharraf in the so-called Red Mosque case was registered two weeks ago on the orders of a judge.
The arrest came after the former president had been granted bail in three other cases and his lawyer said he was free to leave the country.
Musharraf took power in a 1999 coup and later ruled as president until resigning under threat of impeachment by his opponents in 2008. He then went into exile.
He returned to Pakistan in March in a bid to resurrect his political career.