Pakistan's opposition parties, including those led by Benazir Bhutto and Nawaz Sharif, former prime ministers, have called for the judges to be reinstated.
Only four of the Supreme Court's former total of 17 judges agreed to be sworn in under emergency legislation brought in by Musharraf.
The president has been in conflict with the judiciary since he tried to sack Chaudhry in March, a move that led to massive street protests.
He cited "judicial interference" as one of the reasons for imposing emergency rule.
Khalil-ur-Rehman Ramday, one of the judges forced into retirement, told Al Jazeera that paramilitary forces have been stationed outside his home for more than a month.
He said he did not know if he would ever be reinstated but that it was more important to go the "way of one's conscience". Activists expelled
Pakistan has also decided to expel two US human rights activists after they held a vigil calling for an opposition lawyer to be released from detention.
Medea Benjamin and Tighe Barry were picked up by security officials in the eastern city of Lahore on Tuesday and held for several hours before being ordered to leave the country.
"They are revoking our visas and instructed us to leave the country today," Benjamin, an activist from the Code Pink anti-war group, told the Reuters news agency.
"If they can do this to a US citizen who has all kind of liberties and rights, imagine what they can do to their own people," she said.
"This action shows there is no democracy. There is dictatorship. They wanted to terrorise us."
The two activists had been holding a vigil outside the house of Aitzaz Ahsan, an opposition politician and lawyer who was first imprisoned and later placed under house arrest.'Fair' elections
Meanwhile, Pakistan's election commission said on Wednesday that it rejected allegations from leading opposition parties that January's parliamentary elections would be struck by vote rigging.
|There have been frequent protests since |
Chaudry was sacked in March [Reuters]
"The Election Commission is a constitutional body and it is fully independent to hold free, fair and transparent polls," Kanwar Dilshad, the commission's secretary, said.
Bhutto has said that her party is contesting the January 8 polls "under protest" despite fears that they will be massively rigged by the government.
Sharif, who returned from exile from Saudi Arabia on November 25, has been urging other opposition groups to boycott the elections arguing that the vote will not be fair and transparent.
Sharif and Bhutto met in Islamabad on Monday and their parties have been compiling a list of demands that the government must meet to stop them boycotting the poll.
Last week, Musharraf pledged to lift a month-old state of emergency by December 16, ahead of the January 8 vote.
Source: Al Jazeera and agencies