Last week, in a pre-emptive strike before the ABC documentary could air, Nine told viewers a consensual sex incident in 2002 with a 19-year-old New Zealand woman had caused his family "enormous anguish and embarrassment and for that I can't say sorry enough".
But the details of the Four Corners story put Johns and players from the Cronulla Sharks in such a bad light that he has been roundly blasted in media.
The woman at the centre of the story said she had been suicidal following the incident, after other team-mates had participated in group sex.
Today the Nine Network decided to stand Johns down indefinitely from his role on The Footy Show. He has also been suspended from a part-time coaching position with Melbourne Storm.
Nine CEO David Gyngell said, "The fact is, whatever the arguments about the details of the New Zealand incident involving Cronulla players in 2002, the conduct and its aftermath was simply unacceptable, full stop.
"I fully endorse David Gallop's comments concerning the indefensible conduct of some players and the lack of respect for women -- and the critical focus on all stakeholders to help eradicate it from our game. I join with him in extending my apologies and sympathy to the young woman involved in the incident, who clearly is still distressed as a consequence."
"I have always had great regard for Matt, but he knows better than anyone that this incident has placed him in an untenable position. To his credit he has recognised that and acted upon it."
Trouble involving Footy Show hosts is nothing new to Nine with AFL host Sam Newman taken off air last year after an on-air incident in which he ridiculed a female sports journalist with a lingerie-clad mannequin.
Last week the media watchdog ACMA ruled that Newman provoked severe ridicule against the journalist on the grounds of gender. It has instructed Nine to advise it of any complaints regarding Newman and the Footy Show for the next six months.