Human rights observers condemned the closed session of questioning in Islamabad on Tuesday and the lack of details about the allegations against him.
The US-based Human Rights Watch group said the move had created a constitutional crisis and undermined the independence of the judiciary.
House arrest denied
Chaudhary has been confined at his home in Islamabad since Friday, with police blocking most access to him, although the government has denied he is under house arrest.
On Tuesday he was moved to a government guest house before being taken to the supreme court in the capital amid tight security.
The government said on Friday that the Supreme Judicial Council would inquire into "numerous complaints and serious allegations" against Chaudhary, APP news agency reported.
The state-run agency also cited "misconduct and misuse of authority".
Kamal Hyder, Al Jazeera's correspondent in Islamabad, said: "The charges against the judge are primarily of nepotism, that he tried to help his son through his influence, a charge which people say should be levelled on many other ministers."
Lawyers protest
Lawyers across the country have staged angry protests since the government decided to suspend Chaudhary.
Musharraf's government has not released any details of the allegations against the jusge but analysts said the action might be related to his efforts to make authorities account for people who have disappeared after being taken into custody.
Aitzaz Ahsan, a former law minister, told a crowd of about 200 lawyers and opposition supporters outside the supreme court: "We are demonstrating because the judiciary has been defamed by this government action."
Opposition political parties are calling for a national strike on Friday in support of the chief justice.