Tribunal observers fear the court is trying to dismiss those cases in the face of stringent government opposition.
In a statement Thursday, the judges, Siefried Blunk and You Bunleang, called that analysis “baseless” and “nonsensical.”
Government spokesman Phay Siphan dismissed allegations of political influence in the courts in the decision of judges.
Andrew Cayley said a retracting of his statements before a ruling by the Pre-Trial Chamber would be “absolutely meaningless.”
Established in 1984, the holiday acts as a reminder of the crimes of the Khmer Rouge.
The court has come under increased pressure in recent weeks to move forward on cases 003 and 004.
It was unclear how retracting a statement that has already been made public would satisfy the confidentiality requirements of the court.
Around 300 managed to apply to be civil parties in Case Three by the 4 p.m. deadline.
So far, more than 2,000 alleged victims of the regime have applied to take part in the trial.
International prosecutor Andrew Cayley expected to see no more than 10 people on trial.
Reach Sambath fell in his office on Tuesday, suffering an apparent stroke from high blood pressure.
The tribunal has long been split over how many former Khmer Rouge cases it should prosecute.