Cummins said he was surprised to read Khawaja's "allegations" after the latter released his autobiography in the last week, with explosive details about the ball-tampering saga that rocked the cricket world eight years ago.
The Australia skipper finally addressed the topic, after being silent since the revelations came to light, and gave a 68-minute long question-and-answer session to reporters in Sydney.
"When he (Khawaja) says we all knew, if by that he means that we knew sandpaper was going out on the field, he's 100 per cent wrong," Cummins said. "I've said that consistently for the last eight years, I did not know that was happening.
"But I think Usman actually says things that are actually far more serious than that. He says that I and others were architects of a scheme to ball-tamper with sandpaper. That's complete and utter nonsense.
"I was genuinely shocked this week when I found out that Usman admitted that he told Cam (Bancroft) to be careful when using sandpaper. That's not the Usman that I know. It's not the Usman that I think, or that has been part of a team that's helped rebuild this Australian cricket culture over the last eight years, and you know the Usman that would have stopped that from happening there and then.
"Usman's a friend, but friends aren't casual with each other's lives and reputations. In his book, Ussie has been casual with my life and the lives of many others, and I think Australian cricket.
"I support his right to tell a story 100%. I'm really glad that he feels like he can, but we have to be accountable for the things that we say and do."
Khawaja also wrote that he had pushed for the entire team to take collective responsibility for the ball-tampering scandal at Newlands and that two players had not wanted to do so, but Cummins again refuted those suggestions.
Cameron Bancroft, David Warner and Steve Smith, who was captain at the time, were the only players given bans for the incident.
"First part, I don't remember any conversation around collective responsibility," Cummins said. "I don't remember any team meeting where he stood up and said, 'Let's all own this as a team'. So then, to follow on, no, I've got no idea who those two people would be because I don't remember ever being asked or having a conversation about it.
"I've spoken to quite a few other people, and [they are] exactly the same. Trying to piece it all together, no one remembers a team meeting where someone stood up and said, 'We got to all own this'."