His words come after Rooney took to Twitter to claim stories had been leaked about her from information taken from Instagram which was only visible to Vardy's account.
Morgan has expressed concern for the backlash Vardy, who is pregnant, has faced with today seeing her post an Instagram message from a troll wishing death on her unborn baby.
Read more: Who is Rebekah Vardy?
The Good Morning Britain host has spoken out about the war between the WAGs in his Daily Mail column.
Morgan, who claims to "know both women well" lambasted Rooney over the "insensitive" timing of her post.
The father-of-four wrote: "Rebekah’s also seven months pregnant with her fifth child, and is now being bombarded with horrendous abuse from trolls gleefully assuming she is guilty.
"Regardless of whether she is not, this seems a very odd and insensitive time for another mother to publicly shame a long-time friend in this way."
He criticised Rooney's suggestion that the information she was sharing on her private accounts was in fact "private".
Alleging that Rooney had 367 followers on the platform, Morgan said the information was subsequently "public".
He also added that he had spoken with Vardy who was "absolutely adamant" she wasn't the one behind the leak following a public denial.
Vardy has also hit back at Danielle Lloyd today after appearing on This Morning with claims that she'd had similar "run-ins" with Vardy.
She tweeted: "Danielle Lloyd making false claims on @thismorning that we have had ‘similar run-ins’ is utter bollocks. She is just fuming that I ‘didn’t get Jamie recruiting’ for her like she asked me to..."
However, Lloyd retorted: "@RebekahVardy Do you mean like how the sun recruited you Luv! #secretwag we are all entitled to our opinions and we all know it came from your account. Attacking me won’t take that away another low blow by you #notagirlsgirl."