"As for the families of victims, my wish is that you kindly leave your door open for me to make my apologies."
Prosecutors have demanded that Duch, 67, be sentenced to 40 years in jail.
But his defence team have said he was only following orders, and that had he not done so he and family would have been in danger.
"In order to express my most excruciating remorse I have fully and sincerely cooperated with the court whenever it is needed of me," Duch told the court.
Prosecutors have said that Duch's apologies and expressions of sorrow for his actions do not amount to a full guilty plea.
"We submit... that the sentence to be submitted by this trial chamber should be 40 years in prison," prosecutor Bill Smith told judges.
"In imposing this penalty, you are not taking away the accused's humanity but you are giving it back to the victims of S-21," he said.
|An estimated two million Cambodians died under the Khmer Rouge's rule [AFP]
"Let's recall that unlike the prisoners at S-21 he is being met with open and even-handed justice."
Duch, a former maths teacher, has been charged with crimes against humanity, war crimes, torture and premeditated murder.
The case is the first formal trial to delve into the horrors of Cambodia's former Khmer Rouge regime, blamed for the deaths of up to two million people.
Closing arguments in the trial are expected to wrap up later this week, but a verdict is not likely until early 2010.
The maximum sentence available to judges is life in prison.
Duch has been detained since 1999, when an investigative journalist found him working as a Christian aid worker in the jungle.
He was formally arrested by the tribunal in July 2007.
Four other senior Khmer Rouge leaders are in custody awaiting trial.