Sot Troeung, who is 62, told the court he carried letters from Nuon Chea to the head of Tuol Sleng prison, Duch.
Im Chaem did not say who had asked her to retire, but she said her name was withdrawn from a candidate’s list.
Duch told the court Nuon Chea ordered him to execute prisoners at the facility, known to the Khmer Rouge as S-21.
A tribunal spokesman said the list of witnesses who will testify remains confidential.
Defense attorneys have said that the woes over the two cases highlight corruption in the tribunal’s judicial process.
Duch is helping prosecutors describe the inner workings of the Khmer Rouge regime as they seek to tie three suspects to atrocity crimes.
His role in the rise of the Khmer Rouge has not so far been closely examined by the court, and he has never given testimony.
Nuon Chea is on trial for atrocity crimes alongside two other Khmer Rouge leaders, Khieu Samphan and Nuon Chea.
You Bunleng said in a written response Monday the Swiss judge had “committed professional mistakes” and had resigned as a result.
Sam Rainsy told VOA's Khmer service Thursday that officials in the government of Prime Minister Hun Sen "fear a serious investigation."
In a 14-page memo, Kasper-Ansermet said Cambodian staff followed the instructions of his Cambodian counterpart, You Bunleng, only.
Duch said Wednesday that Pol Pot and Nuon Chea “monopolized” decisions on “policy, commerce, the economy and the military.”