Chief executive Roger Lewis says it would be "catastrophic" if a vote of no confidence is passed in the Welsh Rugby Union at Sunday's Extraordinary General Meeting.
Lewis' WRU predecessor David Moffett won enough backing to ensure the meeting was called.
Moffett hoped to win WRU election, but his whereabouts are now uncertain.
WRU chairman David Pickering has also asked clubs to "make sure the mischief makers do not have their way".
Lewis said of a possible vote of no confidence: "If that were to happen - I don't think it would happen - but if it were to happen I think it would be a catastrophic thing for Welsh rugby."
Moffett presented a 17-point manifesto in March which proposed more money for grassroots rugby alongside a better relationship with the nation's four professional regions, and a promise to renegotiate the WRU's debt.
After that Moffett garnered the backing of sufficient clubs - 43 - to force the WRU to call Sunday's meeting in Port Talbot.
He had originally pledged to join and then represent a club at the EGM it is not clear if he will do that now or be there.
The New Zealander has not been heard from since issuing a press release on Sunday, 8 June.
He closed down his Twitter account and website on Monday, posting on it what appeared to be a farewell message.
Moffett also turned down a request made by BBC Wales for a pre-EGM interview.
The 43 clubs want nine issues to be discussed ranging from league structure, to the composition of the board, to debt repayment on the Millennium Stadium.
The clubs accuse the WRU board of not running Welsh rugby in the best interests of the game, and if successful could force a vote of no confidence.
The meeting will go ahead with Lewis confident of seeing off any challenge.
He told BBC Cymru Wales' Gareth Lewis: "We are confident that the clubs will support the Welsh Rugby Union on Sunday because we passionately believe that this is such an important meeting the WRU needs to continue to have its mandate from its members."
But he admits the unrest that brought about the meeting has been a "kick up the backside".
He said the BBC also deserved a "kick up the backside" for the publicity given to Moffett and his supporters, particularly over their analysis of the WRU's finances.
"If you want me to say yes [it's a kick up the backside], I'll say yes to you.
"But what I feel cross about is that yourselves at the BBC have given people the oxygen to promulgate inappropriate, factually incorrect stuff which bears no journalistic scrutiny."
He added: "The financial data that's been published, which has been contradictory over the past few weeks, is the stuff of nonsense... we have tested this with independent third parties and they've told us that this is inaccurate, misinformed, misinterpretation of data and it's clearly misunderstood by the people who disseminate it."
In response to Lewis' comments a BBC spokesperson said: "The BBC provides comprehensive coverage of Welsh rugby, delivering balanced and impartial output across the range of our services to help inform our audiences. We do this through the inclusion of a wide spectrum of views and opinions."
Lewis said the row had been "immensely damaging to Welsh rugby and Wales".
He conceded the WRU "could have done better" over its communication with clubs affected by the proposed leagues revamp that would see divisions reorganised along geographical lines.
However, he accused some of the governing body's detractors of inexcusably bullying leading officials on social media.
Lewis added: "It's been apparent that not all of the clubs shared the view of the league changes and so we have to address that.
"We have to continually be in tune and in touch with our members."
He added: "This has been a campaign orchestrated by a small, very noisy and very personalised group of people who have managed to muster enough votes to call an EGM.
"The result of this campaign will be shown on Sunday and the outcome of the meeting will be what is the state of the game in Wales.
"But what I would say - we respect the voice of the clubs. We respect the call for the EGM."
In a letter to WRU clubs, Pickering said: "It is time for the voices of doom and gloom to be silenced as Welsh rugby must now emerge united and strong for the sake of us all."