Duch, whose real name is Kaing Guek Eav, is on trial for overseeing the torture and execution of about 15,000 people at Tuol Sleng detention centre in the late 1970s.
Duch's confession came a day after a guard, Saom Meth, told the court that he saw his boss beat an inmate with a rattan stick.
"Regarding the testimony of comrade Meth, in general, it is true," Duch told the court.
"The point that I went to torture a prisoner at Tuy (an interrogator's) location, I would not deny it," the 66-year-old former maths teacher said.
But Duch said the most serious crime he committed was the "political indoctrination" of his staff at the prison, also known as S-21, to make them consider the inmates as enemies of the Khmer Rouge party.
"That was the most serious crime that I committed, and that I am responsible for more than 10,000 lives lost at S-21," he said, adding that he was also "the one who initiated" the arrest of many people.
"All the crimes committed at S-21, regardless of forms of torture used and regardless whether the special forces used or transported the prisoners to be executed somewhere else, they had to do it because of my instruction," he said.
"I do not deny all these crimes, I accept them," Duch said, adding that he also used to enter a room where a "very humble" Briton was being interrogated.
Earlier Tuesday, Saom Meth told the court that he heard an ex-colleague report to record-keepers that many foreign prisoners, including Americans, were burned on the street.
The prison in the capital Phnom Penh was at the centre of the Khmer Rouge's brutal campaign of repression and was later turned into a genocide museum after the movement was overthrown by forces backed by neighbouring Vietnam.
Led by Pol Pot, who died in 1998, the Khmer Rouge emptied Cambodia's cities in a bid to forge an agrarian utopia, resulting in the deaths of up to two million people from starvation, overwork and torture.