Alison Hammond made a joke that appeared to be at Phillip Schofield's expense on Thursday's episode of This Morning.
She said she'd "never see" Phil or his co-host Holly Willoughby again when they said goodbye before the duo went on their Christmas break.
It comes amid reports that there is a "toxic" atmosphere on set caused by Phil, which both he and ITV have denied.
When Alison finished her segment in today's show, Holly wished her a "lovely Christmas".
"Thank you and you too, I'm not seeing you again ever," she replied.
But Holly was quick to reassure her, saying: "We'll see you in January it's not that far away."
Phil told her "we love you" and Alison responded that they all love Phil too.
ITV has dismissed rumours of a 'toxic atmosphere' on This Morning as "malicious gossip", insisting there's no issue between Phillip and his co-host Holly.
It was also claimed that Ruth Langsford had made a formal complaint about him.
"It's deeply disappointing and unfair for Phillip to be the target of this sort of malicious gossip," said a spokeswoman for the broadcaster.
"Phillip is a much respected broadcaster and colleague and this is absolutely not a description of This Morning that we recognise.
"Holly and Phil are great friends both on and off screen and are popular among viewers and colleagues alike."
This Morning Editor Martin Frizell hit back at the claims and said Phillip and Holly had a "genuine friendship".
He added: "We have the smartest viewers watching telly and believe me they would be the first to notice any issues — they haven’t because there are none."
