"It is encouraging to see the courts take the unprecedented step of bringing a former Army Chief to account for his alleged involvement in past human rights violations and crimes under international law," Polly Truscott, Amnesty International's deputy Asia-Pacific director, said.
"But Musharraf must be held accountable for all violations committed under his rule, not just a select few," he said.
Musharraf was expected to be formally charged today at an anti-terrorism court in Rawalpindi with criminal conspiracy and murder related to the December 2007 assassination of former Pakistan Prime Minister Benazir Bhutto.
Public Prosecutor Mohammad Azhar told reporters in Rawalpindi today that his indictment would now take place on August 20.
The international human rights body claims to have documented a wide range of rights violations committed during the near 10-year rule of Musharraf in Pakistan between 1999 and 2008.
"Hundreds, if not thousands, 'disappeared' during Musharraf's administration in particular human rights activists documenting violations committed by state security forces and members of armed opposition groups. In his final full year in office, 2007, Musharraf also led a clampdown on the judiciary and independent media," Truscott said.
"His human rights must be protected, just like the thousands of other criminal suspects who faced enforced disappearance, torture and other violations during his rule," Truscott said.
Musharraf was army chief and seized power in a 1999 coup, later he became president and stepped down in 2008.
Bhutto was killed in a gun and suicide bomb attack after an election rally, weeks after she returned to Pakistan from years in self-imposed exile.
A UN commission of inquiry said in a 2010 report that Pakistan failed to properly protect Bhutto or investigate her assassination.
Instead, he was disqualified and became enmeshed in legal cases going back to his regime.
