Pervez Musharraf, who is currently under house arrest, already faces murder charges over the deaths of Benazir Bhutto and a Baloch tribal leader.
He also faces charges over his attempt to sack Pakistan’s higher judiciary in 2007 and the government has said it will try him for treason.
Pervez Musharraf says that all the cases against him are politically motivated.
The latest charge relates to the death of radical cleric Abdul Rashid Ghazi, during the siege of Islamabad’s Red Mosque in 2007.
More than 100 people were killed when Pakistani troops stormed the mosque after a stand-off between troops and hardline Islamists barricaded inside failed.
Analysts say that the storming of the mosque angered hardliners and provoked Taliban militants to launch a bloody campaign of suicide bombings and other attacks on government and security forces.
“The High Court ordered Islamabad police to register murder charges against Musharraf on a petition filed by the son of Rashid Ghazi,” Tariq Asad, a lawyer who represented Abdul Rashid Ghazi, told AFP news agency.
Last month Pervez Musharraf was formally charged in connection with the 2007 assassination of opposition leader and former PM Benazir Bhutto.
It was the first time a current or ex-army chief has been charged with a crime in Pakistan.
Pervez Musharraf denied all the charges set out against him.
In addition:
Pervez Musharraf returned to Pakistan from self-imposed exile earlier this year and is currently under house arrest.
He came to power in 1999 when he ousted PM Nawaz Sharif in a bloodless coup. He ruled the country for nine years before being voted out and then he left Pakistan to live in self-imposed exile in Dubai and London.
Upon his return Pervez Musharraf hoped that he could lead his party into elections, but was disqualified from standing and found himself fighting an array of charges relating to his time in power.
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