Nuon Chea, ex-foreign minister Ieng Sary and former head of state Khieu Samphan all deny charges including genocide and war crimes for the deaths of up to two million people during the regime's 1975-79 reign of terror.
They are also accused of systematically targetting Buddhists, disrobing monks under threat of execution and destroying places of worship.
But Nuon Chea gave judges -- and the hundreds of Cambodians watching from the public gallery -- a very different version of events.
"The question is did we really reject the monks? Of course not," he said. "Some people who accuse Democratic Kampuchea (the Khmer Rouge regime) of destroying religion are wrong. They don't understand the real meaning of religion."
Like Buddha himself, he said, people did not need pagodas to practice their faith because religious principles such as compassion and kindness "are in the hearts of Buddhist followers".
His words stunned the orange-clad clergymen attending the day's session.
"I am quite angry with what he says," said Phnom Penh-based monk Prum Mony, 28, whose grandfather died under the regime. "If he respects monks, why did they destroy pagodas and defrock monks? He is insulting monks."
Fellow monk Lai Sokchea, also 28, said Nuon Chea's revision of history was "a sin" because "his words were different from his actions".
Led by "Brother Number One" Pol Pot, who died in 1998, the Khmer Rouge emptied cities, abolished money and religion and wiped out nearly a quarter of the population through starvation, overwork or execution in a bid to create an agrarian utopia.
Prosecutors last month said witnesses recalled Khmer Rouge leaders labelling monks -- who are revered in Cambodian society -- "blood-sucking parasitic worms".
The tribunal will resume hearing evidence next month.