The former general has faced a roller coaster ride of legal troubles ever since his return to the country in March after four years in self-exile.
The fact that he's being held accountable like any other Pakistani citizen has undermined the once-inviolable position the powerful military has had in Pakistan society.
Musharraf appeared to get a respite from his legal problems Wednesday when a Pakistani court gave him bail in one of three cases in which he had been arrested. Since he had already been given bail in the other two cases, he would be allowed to go free as soon as the paperwork was filed, said his lawyers at the time.
They even spoke of him going to visit his ailing mother in Dubai.
But a spokesman for Musharraf said before he even had a chance to go free, police arrested him Thursday for his alleged role in the death of a radical cleric killed during a raid on a hard-line mosque in Islamabad 2007.
"It is part of a political victimization and nothing else, but we will continue our legal battle to win freedom for Pervez Musharraf," said the spokesman, Mohammed Amjad.
A lawyer for Musharraf, Ahmad Raza Qasuri, confirmed the arrest but said there was no evidence against his client.
"There is nothing to worry about because it is virtually a case of no evidence," Qasuri said. "It was a state action, a military action."
The other cases he faces have to do with his alleged role in the 2007 death of Pakistani politician Benazir Bhutto, the death of a Baluch separatist leader killed by the army, and the detention of Pakistani judges in 2007.
Musharraf ordered the raid against the Red Mosque after students there had begun harassing massage parlors, stores in the capital that sold music and other targets that they felt promoted vulgarity.
The people holed up in the mosque fought for days, and the raid ended with nearly 100 people dead, including at least 10 army commandos. The army seized a large cache of arms from the mosque when the siege was over.
But the incident severely damaged Musharraf's reputation among everyday citizens and earned him the undying hatred of militants who launched a series of punishing attacks following the raid.
The case stems from a complaint filed by the son of the mosque's cleric who died in the siege. The son had been pushing for Musharraf to be investigated but police refused until a judge in Islamabad ordered them to open a case in early September.
Meanwhile, at least seven people were killed in separate bombings in the southwestern city of Quetta and the eastern city of Lahore, police said.
In the most deadly incident, six people died when a bomb exploded outside a police station in Quetta, the capital of the province of Baluchistan, said police official Mohammed Mohsin.
A spokesman for a small separatist group called the United Baluch Liberation Army claimed responsibility for the bombing. Mureed Baluch said the attack targeted the police station in retaliation for what he said was authorities' restricting aid to areas of Baluchistan hit on Sept. 24 by a massive, 7.7-magnitude earthquake.
The earthquake killed at least 376 people. Aid efforts have been hampered by repeated attacks by militants against the Pakistan military as it carries out relief operations.
In Lahore, one person also died when a bomb exploded in a busy market, said police official Raj Tahir.
Associated Press writer Zaheer Babar contributed to this report from Lahore.