Instead, one by one, they were bludgeoned with oxcart axles and then their throats were slashed, he testified.
Former guard Him Huy testified at the trial of Kaing Guek Eav - better known as Duch - who headed the S-21 prison in Phnom Penh. Up to 16,000 people were tortured under Duch's command and later taken away to be killed during the Khmer Rouge's 1975-1979 rule. Only a handful survived.
Him Huy, 54, told the U.N.-backed court that he was assigned to protect executioners while they killed up to 100 prisoners per day.
"The prisoners were told that they were being transferred to live in new homes and were never told that they would be executed," he said.
He said the killings were conducted at night with the detainees shackled and blindfolded as they were taken to the execution grounds at Choeung Ek, nine miles (15 kilometers) from S-21 prison.
After arrival, the prisoners were forced to sit in rooms and then taken one by one to the pits.
"The executioners were instructed to kill the prisoners by asking them to kneel down near the pits. Then they used oxcart axles to strike the back of their necks and later they used knives to slash their throats," he said.
Some 1.7 million Cambodians died of torture, execution, disease and starvation during the Khmer Rouge's rule, during which the Maoist idealogues emptied cities and forced virtually the entire population to work in farm collectives.
Duch (pronounced DOIK), 66, is the first senior Khmer Rouge figure to face trial and the only one to acknowledge responsibility for his actions. He is charged with crimes against humanity and is the first of five defendants scheduled for long-delayed trials by the tribunal.
Senior leaders Khieu Samphan, Nuon Chea, Ieng Sary and Ieng Sary's wife, Ieng Thirith, are detained and are likely to face trial in the next year or two.
Him Huy said he joined the Khmer Rouge movement in 1973. He was assigned to S-21 a year after the movement's victory in 1975.
He told judge Jean-Marc Lavergne that he was trained how to kill the prisoners by Duch himself and one of his deputies. He said Duch personally visited Choeung Ek twice.
"There was a mass killing, and he (Duch) visited that location and it was almost dawn. Sitting near the pits, there was my leader, Duch," Him Huy said.
He said he killed only one prisoner, upon receiving an order from Duch and his deputy to help other executioners finish the killings because it was almost dawn.
Him Huy, who said he was terrified of Duch, is the second senior S-21 staff member to testify against his former boss. On Wednesday, a senior interrogator, Mam Nai, said he feared that the regime would one day even turn on him and order his execution. He denied using torture to extract confessions from the prisoners.
Mam Nai broke down in tears when recalling the deaths of family members and some, including one of his former teachers, who perished at S-21. He said his brothers, first wife and children were killed by the Khmer Rouge.