Mr Skene predicted the trust would lose at least 7 per cent of its revenue if the increase went ahead.
"It's just outrageous - the impact will be extensive," Mr Skene said. "We'll be looking at $30,000 a year in fees - that's money being directly taken away from the community.
"I'm going to have to tell some sports clubs they won't be getting funded this year."
Mr Skene said the trust had also funded non-profit organisations such as Supergrans, the Wairarapa Community Law Centre, the Wairarapa Free Budgeting Service and the Heart Foundation, as well as various schools.
"There'll be less money to go around for our kids, too."
Trust House is another major lessor of gaming machines in Wairarapa, collecting $2.5 million worth of community grants in 2014.
Chief executive Allan Pollard said the fee hike was "not ideal" and was concerned rural trusts and societies supplying smaller, less profitable gaming venues would be hit.
"If smaller gaming halls aren't making a profit on their machines and can't keep up with the fees, they won't keep them," Mr Pollard said. "If fees continue to increase, there may come a day when gaming halls will only be in [urban] areas."
The Gambling Commission required 80 per cent of revenue from pokies be distributed in the areas where the revenue was generated - meaning rural areas would "miss out" if machine numbers dropped.
"It's important we keep that money in Wairarapa," Mr Pollard said.
"Without it, it'll leave a big hole for other funders to pick up."
The Problem Gambling Foundation has welcomed the hike and hopes it will lead to increased compliance of a sector which, according to chief executive Graeme Ramsey, has been "a story of poor customer care".
He said a "mystery shop" by the Department of Internal Affairs had found the "vast majority" of pokie operators were in breach of the Gambling Act.
"The department hasn't increased fees since about 2007, but it can't decrease its compliance efforts - not when the sector hasn't stuck to its legal responsibilities.
"They've brought this on themselves."
But at the Prime Community Trust, Mr Skene plans on making a "strong submission" to the department.
"I can't see the justification - the department has electronic systems in place, so direct regulatory control should have decreased.
"We are a compliant operator, and we won't be getting that level of service - but we'll be walloped by the cost."