Tullis Russell managing director Don Munro said the firms bill had risen from 16,300 to nearly 70,000.
The price rises, which have also affected other paper manufacturers and businesses in Scotland, follow the merger in 2002 of the North, East & West regional authorities to form a single authority, Scottish Water.
A spokeswoman for Scottish Water said the firm had altered its tariffs to make them reflect the costs associated with offering the water and waste service.
The firm was willing to meet with clients to explain the charges, but she stressed that they were lower than they would have been under the three previous bodies.
Munro said Scottish Water had been told to write down a substantial amount of debt. As a result, price rises had been passed onto businesses instead of being applied to household consumers.
Its not a matter of life or death for us, but when you pile on all the additional costs we have suffered, it adds to the burden, he said.
Montgomery Litho group finance director Andrew Montgomery said his company had been in dispute with Scottish Water over a 12,000 bill for more than a year.
The cost of water has gone through the roof and they [Scottish Water] are just not willing to explain, he said. Scottish Water is threatening legal action, which doesnt bother me, but it seems they want to bully companies into paying these extortionate bills. I fear for the small printer.
Story by Andy Scott