The new charges involve a crackdown on a pro-Taliban mosque in Islamabad in 2007 in which about 100 people died, the Los Angeles Times reported Thursday.
Musharraf had paid about $19,500 in bail Wednesday on charges in the killing of separatist leader Nawab Akbar Bugti in Baluchistan province.
He also had been granted bail in two other cases.
A senior Islamabad police official said Musharraf would appear in court Friday.
The latest charges were filed a month ago by Haroon Rashid, who claims Musharraf contributed to the death of his father, Abdul Rashid Ghazi, who was the imam of the mosque.
In an affidavit, Rashid said more than 300 witnesses had testified the operation was conducted at Musharraf's direction.
Notable deaths of 2014 [PHOTOS]