Musharraf said in a TV interview on Tuesday that Chaudhary had tried to remove him illegally and the country would have "landed in chaos" if the former Chief Justice had been allowed to have his way.
The President's comments prompted a swift reaction from Chaudhary, who termed Musharraf's statement as "absolutely incorrect".
"The statement of General (retired) Pervez Musharraf that the Chief Justice of Pakistan wanted to remove him illegally is absolutely incorrect simply for the reason that I was not a member of the bench which comprised 11 honourable judges (four have since taken oath under the PCO) and the case which was still being heard was to continue on Monday, November 5, 2007," Chaudhary said in a statement.
"This is the same Supreme Court which decided in favour of General (retired) Musharraf on his dual office case and I was not a member of that bench and the decision was applauded."
Chaudhary has been under house arrest in his official residence since November 3, when he was sacked for refusing to endorse the emergency. Around 50 judges have been dismissed for refusing to take an oath of loyalty to Musharraf.