"May I be permitted to apologise to the survivors of the regime and families of the victims who had loved ones who died brutally at S-21. I would like you to forgive me," Duch told the panel of five judges.
An estimated 1.7 million Cambodians died during the Khmer Rouge's rule over Cambodia, from 1975-79.
Speaking before a packed courtroom Duch said he wanted "to express regret and my heartfelt sorrow for all the crimes committed".
But he added he was only following orders issued by the top Khmer Rouge leadership, and had feared for the lives of his family if he had disobeyed.
"I am solely responsible for this crime, but I am just a scapegoat. A person who played a role in the killings," he told the court.
Duch, 66, is the first of five senior Khmer Rouge leaders to stand trial before a special United Nations-backed tribunal, three decades after the regime's reign of terror.
Earlier prosecutors opened their case against the former prison chief, saying that "history demands" justice for the victims of the Khmer Rouge.
"Justice will be done," Chea Leang, the co-prosecutor, said at the start of the second day of the long-awaited trial.
He said Duch and the S-21 prison he ran had played central roles in the Khmer Rouge's iron-fisted rule.
"S-21 formed an integral and indeed vital role in a widespread attack on the population of Cambodia," Chea Leang told the court.
"The accused's crimes were part of this attack."
"For 30 years, one-and-a-half million victims of the Khmer Rouge have been demanding justice for their suffering. For 30 years, the survivors of Democratic Kampuchea have been waiting for accountability," he said.
"For 30 years, a generation of Cambodians have been struggling to get answers for their fate."
|Some 1.7 million people were killed during the Khmer Rouge's reign of terror [Reuters]
The first day of the trial on Monday saw no witness testimony and Duch spoke briefly only to confirm his identity and his understanding of the charges against him.
As well as hearing from his victims, Duch's own testimony is expected to be vital in securing the convictions of the four other Khmer Rouge leaders awaiting trial before the tribunal.
The group includes Nuon Chea, the Khmer Rouge's former deputy leader; Khieu Samphan, the former Khmer Rouge head of state; Ieng Sary, the former foreign minister; and his wife, Ieng Thirith, who was the regime's social affairs minister.
On Monday the prosecution read out a 45-page indictment against Duch that contained a litany of grisly accounts of the alleged atrocities committed under the Khmer Rouge rule.
The Khmer Rouge executioners threw victims to their deaths, bludgeoned them and then slit their bellies, or had medics draw so much blood that their lives drained away, prosecutors said.
Duch himself allegedly oversaw the atrocities, which included snatching children from their parents and dropping them from the third floor of a prison building to break their necks.
Prosecutors alleged that Duch's job was to extract confessions of counter-revolutionary activity but said that "every prisoner who arrived at S-21 was destined for execution".
"Several witnesses said that prisoners were killed using steel clubs, cart axles, and water pipes to hit the base of their necks," the indictment said.
"Prisoners were then kicked into the pits, where their handcuffs were removed. Finally the guards either cut open their bellies or their throats."
The indictment also claims that some prisoners were killed by having large quantities of blood withdrawn by medics, leaving them "unconscious and gasping".
Professor Alex Hinton of Rutgers University's Center for the Study of Genocide and Human Rights, said the indictment set out in more detail than ever before the atrocities committed by the Khmer Rouge and was a critical historical record.
"They took the lifeblood of people. I think it really encapsulates the utter dehumanisation," he said.