A former head of the company has been accused of making threatening phone calls to industry participants in the talks.
The allegations have emerged at an Upper House inquiry scrutinising the Tasmanian Forests Agreement Bill.
The agreement is designed to end the state's forest wars by protecting half a million hectares of trees from logging.
"My CEO Terry Edwards had received a number of phone calls from the CEO of Gunns which could only be called threatening, with respect to his involvement in this process and FIAT's involvement in the process," he told the inquiry.
"From our point of view, if I can put it in the vernacular, Gunns was going rogue.
"In other words they weren't acting as an industry participant anymore, they were acting solely in their own interests."
Mr Amos says the former chief executive of the National Association of Forest Industries, Allan Hansard, received similar phone calls.
The head of Gunns at the time was Greg L'Estrange.
He has told the ABC the phone calls took place when the company was a FIAT member.
Mr L'Estrange says Gunns provided about two-thirds of the lobby group's income and felt entitled to express a view on the peace process.
Gunns severed its ties with FIAT in September 2010.
Tasmania's lucrative speciality timber industry is urging Upper House MPs to amend the forest peace deal legislation.
The sector employs more than 2,000 full-time equivalents.
The inquiry heard it contributes hundreds of millions of dollars to Tasmania's economy every year and is larger than veneer producer Ta Ann.
The president of the , Andrew Denman, says the sector will be wiped out if the legislation is passed.
He says the push to expand Tasmania's Wilderness World Heritage Area by 170,000 hectares is an added concern.
"I know it's probably a horrible way to say it, but it gobbles up the majority of our speciality timber areas and leaves us with virtually nothing," he said.
"Now what I would like to ask of the signatories, through you, is what work has actually been done to ensure that the speciality timber sector will have enough timber after these reserves have been put in place?"
He says uncertainty over wood supply is already hampering talks with a potential client in Asia who wants a new boat.
"So what am I going to tell Mr Hong Kong?: 'Sorry, we are closed for business, I can't do it, I can't get your timber'."
"He'll go somewhere else. That's $800,000 worth of work that Tasmania's going to miss out on because we don't have a guaranteed supply.
"That's food on the table for my guys, it's mortgage payments, it's school fees, it's car payments, all gone."
Upper House MPs have been warned against "unpicking" the forest peace deal.
Parcels of land earmarked for protection have to be approved as part of enabling legislation.
But Jim Adams from Timber Communities Australia has urged Legislative Councillors not to make major changes.
"I mean if there was proposals to withdraw this area, withdraw that area, withdraw various areas and it started to look like a much smaller number, I'm sure there would come a point where environmental groups would say 'well that's not the agreement we agreed to'."
"In fact, probably all of the signatories would get to a point where we would have to say 'that's not the agreement that we arrived at'," Mr Adams said.