Almost 200 local businesses are facing a doubling in waste charges.
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M.T. Bins owner, Michael Knight, has already been wearing the cost of last year's increased charges.
But with the proposed changes doubling from $100 per tonne to $200, he says his business likely wouldn't survive.
"It is the Katherine community that will wear the cost," he said.
"We are already paying $500 a day in tip fees. That is going to increase to $1000. Which small business can deal with that sort of cost?"
The local waste collection service, which began in 2005 with just one skip truck, picks up rubbish from Katherine's restaurants, properties on Edith Farms Road, small businesses, tourist parks, not-for-profit organisations and even schools.
The rubbish is then taken to Katherine's waste facility, which is ageing and at capacity.
"Council needs to fund the relocation of the (rubbish) site, that is their excuse for raising the money," Mr Knight said.
"My argument is they've dragged these numbers out of thin air and there is no saying who has made these estimates."
"Darwin charges just $80 per tonne and that is with a whole range of services from recycling to a tip shop. Katherine gets a big hole in the ground and no service what-so ever.
"Council is holding everyone to ransom."
A new waste facility for Katherine is expected to cost Katherine Town Council about $40 million.
In preparation, the council has also set out a series of rate rises, which has caused an uproar in the town.
Mr Knight said he sees a future where local businesses and some property owners will be unable to afford having their rubbish collected.
"We can't run at a loss," Mr Knight said.
"We either pass on the cost or get out of the business."
Despite being concerned and frustrated at the prospect of charging more for services or losing customers, Mr Knight said he is adamant to continue in the business "as best we can".
"We have been here for 15 years and we are dedicated to the town," he said.
"If this rise in cost goes ahead it is only going to add to the discouraged feeling in town."
Katherine Town Council has been contacted for comment.
Katherine Town Council's proposed municipal plan is out for public comment, closing on June 26.
Written submissions can be made direct to the Civic Centre or emailed records@ktc.nt.gov.au
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