As reported in these pages, the retired official caused outrage on Jamie Vardy's podcast this week when he described playing games with himself during Premier League matches, including seeing how long he could avoid blowing his whistle or leaving the centre circle.
Those comments drew widespread condemnation, prompting calls for an FA investigation and public criticism from several of his former colleagues.
Dean has now moved to clarify his position in a statement posted to social media.
"Throughout my 25 years as a professional referee, I have always applied the Laws of the Game to the best of my ability," he wrote. "My approach as a referee was always to allow the game to flow and whenever possible I preferred to apply a high threshold for contact which the players liked.
"However, if I saw a foul challenge that needed me to take the appropriate action I would give it from the correct position. At no stage was it my intention to question, criticise or undermine the integrity of refereeing in this country. I have always respected the profession and the responsibility that comes with being a referee."
The statement follows sharp criticism from fellow former Premier League official Graham Scott, who dismissed Dean's original claims as "nonsense" in an interview with talkSPORT.
"I worked with Mike loads at times, they're not true stories," Scott said. "It's kind of the audio equivalent of clickbait isn't it, to try and get people interested and laughing. It's palpable nonsense.
"Mike Dean was of course an outstanding ref, but it makes it so much harder when retired referees either bash their former colleagues for the sake of it. It's fine to criticise, I do that, but do it with a bit of context and a bit of empathy."
Scott went further, directly challenging his former colleague to repeat the claims in front of current officials.
"I challenge Mike and say, 'Okay, would you stand in front of the current refs and repeat all of those things?'" he said. "And of course he wouldn't, because they're not true."
Dean's clarification has done little to fully quell the row, with questions still lingering over whether the FA will look further into the original comments.