Mr Gordon told the Rotorua Daily Post he was "astonished and concerned" to read the statement in the media as it was the first he had heard of it.
"I have had no notification from my employer - the chamber board chair and its members. I have been on leave over the last few weeks, some of which has been recommended medically."
Chamber executive member Jonathan Temm said the chamber did not wish to publicly respond to Mr Gordon's claim.
Mr Gordon said there was an employment dispute in process.
"At the end of last year I raised issues of concern with the chamber board related to their understanding of governance and management.
"This progressed to an employment dispute.
"By way of a January 8 newspaper article I discovered the board's intention to restructure the chamber - I had no prior knowledge or communication on this."
Mr Gordon said the chamber's reputation was critical to him as could be seen by his "commitment and service of nine years".
"I will fully respond to this attack on my reputation and credibility and appreciate the support I am receiving from members."
Rotorua Mayor Steve Chadwick said Mr Gordon and the council had had their moments over the years, "but some occasional healthy tension is not necessarily a bad thing".
"However, overwhelmingly under Roger's leadership, the relationship has been professional and directed towards a shared vision of re-energising business activity in Rotorua.
"He has been a proud flag- waver for Rotorua business and during his time at the helm the Chamber of Commerce has grown substantially. Roger's departure heralds a new era for the chamber, a situation we are also in at the council.
"I want to acknowledge his service to business in our community and his advocacy for local business organisations."
Mrs Hawker said the chamber would be advertising and seeking suitable applicants for a general manager position.