In an open letter to Musharraf to coincide with the anniversary of his seizing power in a bloodless coup on 12 October, 1999, the New York-based Human Rights Watch (HRW) called on the president to return Pakistan to constitutional rule without delay.
The letter accused Pakistani military agencies of torturing and harassing political opponents, journalists and former government officials.
It also highlighted a surge in religious extremism and sectarian killings that HRW blamed in part on the Musharraf administration's policy of marginalising mainstream opposition political groups.
"In Pakistan, the judiciary has been emasculated, political parties rendered powerless, and extremist and sectarian religious parties strengthened under Musharraf's rule," said Brad Adams, executive director of HRW's Asia Division.
"General Musharraf should transfer power to a legitimate government now," Adams said, adding that Pakistan's collaboration in the US war on terror had been exemplified by a disregard for due process.
"Arbitrary arrests and detentions, allegedly with the support of US authorities in Pakistan, have taken place with depressing regularity"
Executive director of HRW's Asia Division
"Arbitrary arrests and detentions, allegedly with the support of US authorities in Pakistan, have taken place with depressing regularity," he said.
Denounced by many in the West as a usurper and dictator when he ousted then Prime Minister Nawaz Sharif in 1999, Musharraf became a close ally of the US in the wake of the 11 September, 2001 attacks, when Pakistan joined a coalition against its former allies in neighbouring Afghanistan, the Taliban.