She insisted that this is not a joke and continued to lash out at the host.
Jenner stopped the interview and took the time to put Morgan down for the remark.
Jenner starts to answer the question but breaks off to reprimand Morgan, to which he smiles and shrugs his shoulders.
The 68-year-old star fired back saying, "See you made a comment there and that is why you would get in trouble. OK?"
Speaking about being transgender, Caitlyn who is Piers Morgan's first ever transgender guest said: "Actually Piers we have a lot to talk about because I think you represent a lot of people out there who don't understand this issue and exactly what it is".
Adding: "It's not something that you joke about".
After asking why it is inappropriate to comment on or joke about a trans person's genitals, Jenner gets visibly angry and replies: "Because it's not amusing". It's part of my life and it's a very serious part of my life.
Piers then asked: "How does your physique compare now".
"You don't make a joke about that because it's not amusing, it's life", Jenner said. Upon receiving her "edited copy", Kim said Caitlyn was "not a good person" and called her a "liar". It's something as I said before - [this is] serious stuff, people die over these issues.
The reality TV star, who initially found fame as Olympian Bruce Jenner, let rip during a chat with Piers Morgan.
"Tell me if I am going too far, but do you have sex now?" he asks, to which Jenner snaps back: "You are going too far, it is absolutely none of your business".
Apparently Caitlyn Jenner didn't tell the Kardashians about her sexual reassignment surgery because she didn't trust them. "It does take me a little longer to get ready in the morning".
The full interview will premiere tomorrow on ITV.
Piers asked whether she didn't trust the Kardashians, Caitlyn said: "Of course not - of course I didn't trust them, yeah".
Addressing the current state of his relationship with the children his ex-wife welcomed with her late husband Robert Kardashian, she explained: 'I just don't communicate with them like I used to.
"Trans bodies have boundaries and trans lives have edges that deserve respect".
He said: 'You have six children. "I want my voice to be heard and I want to see if I can make a difference". "I met Khloé when she was five years old". I didn't want them to leak it to the press, OK?
Morgan defended his comment much to Caitlyn's annoyance.