A tribunal spokesman said Duch was moved to tears as he led the officials through the "killing field" at Choeung Ek, a site where most of the S-21 prisoners were executed and dumped in shallow mass graves.
Reach Sambath said Duch wept during the three-and-a-half hour visit as "the accused explained what happened ... when he was the chief of S-21".
"We noticed that he was feeling pity, tears were rolling down his face two or three times"
Reach Sambath, tribunal spokesman
"We noticed that he was feeling pity, tears were rolling down his face two or three times."
Sambath said Duch was especially moved when he stood before a tree with a sign describing how executioners disposed of their child victims by bashing their heads against its trunk.
The visits were part of a re-enactment by the international tribunal of investigating judges meant to get the accused to explain past events.
Duch, 65, is facing charges of crimes against humanity for his role as commandant of the Khmer Rouge's largest detention and interrogation facility during the Khmer Rouge's rule over Cambodia between 1975 and 1979.
Wednesday's prison visit was closed to the public and media, but three S-21 survivors joined tribunal officials.
The three said they did not harbour anger toward Duch but hoped to face him during the trip to ask why they had been imprisoned and tormented.
Bou Meng, 67, said he and his wife, Ma Yoeun, were both put in S-21 prison in 1977 and that his wife was later executed.
"I just want to ask him what she may have done wrong that they had to kill her. Where is my wife?" said Bou Meng, who was spared because he could paint Pol Pot portraits.
Pol Pot, the Khmer Rouge leader, died in 1998.
Duch is the lowest ranking of five former Khmer Rouge leaders being held for trial, but his role in charge of S-21 has made him one of the most notorious.
He has insisted that he was simply following orders to save his own life.
"Tuol Sleng is a living nightmare for us"
Youk Chhang, Documentation Centre of Cambodia
The S-21 prison is now a genocide museum, and its walls are lined with pictures of prisoners who died there.
Some 17,000 people are thought to have passed through S-21, with only 14 said to have survived.
Commenting on the prison visit, Youk Chhang, the director of the Documentation Centre of Cambodia, which researches alleged Khmer Rouge atrocities, said Duch was not going to "see blood stains or hear the scream of prisoners any more".
"Tuol Sleng is a living nightmare for us."
Born in the early 1940s, Duch trained as a teacher before joining the Khmer Rouge
During Khmer Rouge rule between 1975 and 1979 he headed the regime's Santebal secret police
He also headed the notorious S-21 torture and interrogation centre in a former Phnom Penh high school
Prosecutors say Duch's name appears on dozens of execution warrants
Duch fled Phnom Penh when Vietnamese forces invaded in early 1979
Living in a remote jungle hideout, he converted to Christianity in 1996
In 1999 he was arrested and charged with murder, torture and membership of an outlawed group
In 2007 Duch became the first suspect brought before the UN-backed tribunal to try former Khmer Rouge officials