Mr Petersen said they had had four years and 48 weeks to raise concerns, but instead they left it until the last minute.
"If they are unhappy, it would have been nice if they had become involved earlier instead of the last four weeks of a five year term."
Despite the opposition, Mr Petersen remained confident farmers would support the levy referendum vote.
Farmers had been listened to and the proposal had been amended accordingly, while maintaining its core functions of market access, research and development and market development.
Opposition to Meat and Wool continuing in its current form has been led by Southlander Murray Turner and Hawkes Bay farmer Robin Hilson, and centre around a perception the board lacks credibility and transparency.
There are also concerns it is costly to run.
Mr Hilson said the board had spent $1 billion in the past 18 years for little or no gain.
He and Mr Turner want to restructure the body along the lines of the Foundation for Arable Research, to focus solely on funding research and development.
Under their proposal, the marketing of wool and meat would be left to export companies and trade access would be left to the Ministry of Foreign Affairs and Trade.
Asked if this hands-off approach by farmers risked repeating the mistakes of wool, which had a decade of little or no marketing, Mr Hilson said previous efforts had been expensive and they had not worked.
Once farmers sold prime stock to a processor, it became their responsibility.
"My responsibility is to meet the requirements that he wants, and his business succeeds or fails on how successful he is in marketing and selling that product," he said.
Mr Petersen said this was the first time opposition this vocal had campaigned against the producer board, and he believed it was the result of frustration at issues such as low wool prices and the lack of change in the meat industry.
"We are getting farmers expressing huge frustration with both these issues and using this to voice their displeasure at the current state of their industry."
Romney New Zealand had also entered the fray, but Mr Petersen said that was based on the view that Meat and Wool was favouring wool exporter Wool Partners International over Elders Wool in what had become acrimonious competition.
Should the vote go against the board, Mr Petersen said he would be accountable.
He would also recommend the consultation process be repeated, with farmers being presented with a new proposal.
Such a step would be complicated, problematic and expensive, but could be done.
Should farmers give a favourable vote, Mr Petersen said Meat and Wool needed to explain better to farmers its role and its core activities.
"The perception is we're high cost. I don't believe that's the case."
He would also seek a quicker time frame for meat companies to take up a greater share of meat marketing funding than the five years he originally proposed.