The case was brought by the Environment Agency.
The Southern Counties Fresh Foods abattoir, based at Langport, Somerset, and owned by RWM Food Group, had been asked to make improvements to reduce the risk of pollution. It also been required but failed to submit an accident management plan.
Richard Phelps, managing director of Southern Counties Fresh Foods, said the size of the fine left him "absolutely gutted."
He told MTJ: "In our opinion it appears to be high and we think the Environment Agency wanted to make an example of us. The fine is purely for failing to respond to a paper chase audit. There was a breakdown in communication but there was no risk whatsoever of pollution." Phelps added that the fine should serve as a warning to other abattoirs to keep paperwork in order.
Colin Tew for the Environment Agency said: "The abattoir holds polluting substances like blood, oil and chemicals and is situated alongside a significant watercourse.
"In each of the failures by the defendant to comply with the terms of the permit, its conduct fell very significantly below the standards required of it and to be expected of a company of its size and experience working in such an industry.
"We hope that significant improvements will now be made to the management system to ensure that these failures are not repeated."
RWM Food Group was fined £24,000 and ordered to pay costs of £977 by Yeovil Magistrates after admitting three charges of failing to comply with an Enforcement Notice contrary to Regulation 32(1) of the Pollution Prevention and Control (England and Wales) Regulation 2000 made under Section 2 of the Pollution Prevention and Control Act 1999.