Whyte was in charge of Rangers when they went into administration in 2011 before Green took over with a consortium last year.
However, Whyte recently claimed that Green was his "frontman" for the takeover and that he is still the majority shareholder at Ibrox.
"That he, after all he did to damage Rangers and the club's vast and loyal support, should attempt to denigrate those who stepped in to pick up the pieces and begin what will be a huge restructuring of the club at all levels is deeply disappointing but predictable," Green said in a statement on the club's official website.
"We all need to be absolutely clear on what is happening. These are distorted and malicious allegations coming from a man who is completely discredited and now under police investigation.
"He claims I was his front man. He could not be more wrong. With 8%, I am the major shareholder in Rangers FC and I have no tie in of any kind with Mr Whyte."
Rangers manager Ally McCoist has said that he will speak with Green in order to gain some clarification over the matter.