Pakistan's Supreme Court has urged the government to release dozens of people rounded up by the intelligence agencies in the US-led war against terror.
Chief Justice Chaudhry was reinstated after suspension
Chief Justice Iftikhar Chaudhry said there was "overwhelming evidence" that many missing people were being held in government custody.
President Musharraf suspended Mr Chaudhry earlier this year.
But he was reinstated in July and has become a key figure of opposition to the president.
Before his suspension, Mr Chaudhry had taken up the cases of missing people believed to be in government custody.
It was one of a number of issues that saw him and the government being drawn into conflict.
Mr Chaudhry made his comments on Tuesday while hearing petitions from some 40 families seeking the whereabouts of their missing relatives.
He said the government had to charge them or release them.
"It has been established that these people are in the custody of (spy) agencies," Mr Chaudhry said, the Associated Press news agency reports.
"Choose a respectable way and release all the missing persons... we have overwhelming evidence that people are in your custody," he told the deputy attorney general.
Hundreds of people have gone missing in Pakistan since 2001 after Pakistan decided to support the US war on terror in the wake of the 11 September attacks.
Rights groups say they are illegally detained by security agencies for alleged links with radical groups.