Broadcasting from London following the Queen's death, the hosts were interviewing former royal protection officer Simon Morgan about the terror threat level for the Queen's funeral.
The interview however turned flirtatious when Ally said to Simon, "Did I tell you you're very handsome?"
Simon and Ally then giggled as she held up her hand and he said he normally had a face for radio.
While the pair continued to laugh, Karl shifted uncomfortably in his seat before having a dig at his co-host.
"I am watching you guys flirt, that is torture, in front of the nation," he said.
"Be more respectful please, it is disgusting," he added jokingly as the pair continued to giggle.
The Today hosts often take cheeky jabs at each other, with Karl poking fun at his co-host telling her she sounded "condescending" during the show last month.
Scherri-Lee Biggs, a former Miss Universe Australia and Celebrity Apprentice contestant, was reporting from Kingfisher Bay Resort on Fraser Island for the Today show when she got confused and stumbled on her words.
“Guys, I just want to tell you that it is really lovely because this resort was actually built after I was born,” she said before she began to second guess herself.
“No, before. No, after. I don't know,” she laughed. “My brain is coming back from holiday.”
“If you are going to rub in how young you are, you do want to get that right,” Karl remarked.
Allison then jumped in to try and help Scherri-Lee figure it out by asking her how old she was.
“I am 32, in two weeks,” she replied, confirming that the resort was built before she was born. “Thank you, Ally.”
“Here to help, sweetheart,” Allison responded, which left Karl stunned.
“Gee, that sounded condescending,” he remarked.
“I definitely didn’t mean it to be!” Allison quickly replied.
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