"I have met so many mothers and their children that they have put their hand on their heart to me and said 'Hey Pete, my boy or little girl was a healthy, functioning, beautiful child – and they're still a beautiful child, but something happened'," he said.
"When they got a shot one day, and within two hours, 12 hours or 24 – 48 hours, that little boy or girl completely changed their behaviour, completely changed their nature."
He then added: "Before everyone's going 'shut up Pete Evans', I believe in vaccines and I believe in safety of vaccines, I think there are amazing vaccines out there, but it doesn't seem to work for everybody. There seems to be people affected by it."
Seemingly agreeing with his statement, Kyle added: "It's like the COVID-19 thing. Some people end up in hospital on respirators, or dead, and some people get it and have no symptoms at all."
At one point, Kyle also suggested that people need to "do their own research" to make decisions on whether to vaccinate their children.
"People need to do their own research on this. I know people who are like 'Oh, you've gotta have your kids vaccinated against measles, mumps all this' and others who say 'Well I won't be vaccinating my kids'. It's one of those real split down the middle type of opinions with families," he said.
On Twitter, one listener said they switched off their radio in frustration when the segment aired, while another suggested that perhaps it was time to target their advertisers "as a matter of urgent public health" if they continue to promote Pete Evans' medical views.
Later in the interview, Evans seemingly made reference to a bizarre recent conspiracy theory he posted about COVID-19, saying the media coverage of the virus "doesn't make sense".
Earlier this month, the chef had shared a detailed list which urged people to "look out for" certain code words and implied "mass trials" and "executions" were happening behind closed doors.
"How come our health minister, how come our government, how come the mainstream media over the last three to four months, have not one time talked about how to keep or build a strong, healthy, robust immune system with the information we must have?" He questioned.
"It certainly does make you think … Because what we're fed by everyone and what we've thought our whole lives, sometimes is wrong," Kyle offered.
Responding to the interview, Royal Australian College of GPs president Dr Harry Nespolon told news.com.au Kyle and Jackie O's move was "extremely disappointing".
"Mr Evans may consider himself 'pro-choice for medical freedom' but the fact that his assertions were by all accounts barely challenged by the radio hosts makes this interview particularly problematic," Dr Nespolon said.
"I think that all television networks, radio stations and publications have a responsibility to self-regulate and not provide platforms to people spreading dangerous and misleading information that can harm public health.
"If they do interview such individuals they need to at least challenge conspiracy theories and 'advice' contrary to expert medical opinion," he added.
In a statement issued to news.com.au, an Australian Radio National spokesperson defended the segment.
"The Kyle & Jackie O Show had Pete Evans on the show today as a celebrity guest to discuss a range of topics," the statement read.
"This is a light entertainment radio show where celebrity guests often share their personal views and stories as part of an entertainment format."
Last week, Michelle Bridges and Jackie O both spoke out in defence of the embattled chef, insisting he's not a "crazy loon".
During an interview with Bridges on KIIS FM, Jackie O raised the topic of Evans and said she felt sorry for him.
"What do you think about Pete (Evans)?" Jackie asked. "I actually feel a little sorry for him.
"I think in the media they've painted him as some crazy loon and he's not at all. He's just into health and … looking at alternatives.
"They really are going so hard on him, I think it's really unfair," Jackie O said.
It comes shortly after Evans insisted he's not an anti-vaxxer while sharing a link to a petition calling for Australians to stop being "medicated" by flu vaccination.
"Stop coercion of Australians to be medicated with influenza vaccinations," he wrote on Instagram.
"I have been sent so many messages about this subject in the last few days and heard such heartbreaking stories.
"If you feel it in your heart to say what you feel, then a petition has been released with federal parliament to stop the mandatory injection for nursing home visitors.
"There are apparently studies linking the flu injection to an increased possibility of other illnesses. Someone may like to produce that evidence if there is any below in the comments?"
It's the second public backlash Kyle and Jackie O have been at the center of in the past 24 hours, after an angry viewer reaction to their sit-down interview on 60 Minutes last night.
Nine had teased that Kyle was poised to reveal a serious, secret health diagnosis in the interview – but when viewers tuned in they found it was merely a prank he'd played on his co-host.
