The foot-and-mouth outbreak originated at Pirbright in Surrey
The county council at the centre of last year's outbreak of foot-and-mouth disease has said it is "upset" to have been left with a £250,000 bill.
Surrey County Council (SCC) said it was disappointed the government had not reimbursed it for the hard work put in to stop the spread of the disease.
Eight farms were infected with the disease which escaped from laboratories run by the government at Pirbright.
The government said local authorities already had funding for emergencies.
David Harmer, SCC executive member for the environment, said the council had to cut back elsewhere as a result of the £250,000 "black hole".
"Trading Standards reluctantly had to reduce the service it offered in lower priority areas for a while - such as dealing with business inquiries and recruitment for the approved trader scheme," he said.
"This comes six months after government funding for animal welfare and health to Surrey and other local authorities was cut by some 12%."
The Department for Environment, Food and Rural Affairs (Defra) said it recognised the good work local authorities did in dealing with disease and the close co-operation it had developed with them.
But it added: "Operating partners in the public sector who are involved in emergency response should seek any extra funding required through their own normal funding channels.
"The revenue support grant makes some provision for emergencies.
"Local authorities make their own arrangements for allocating the funding internally.
"Where local authorities act during an emergency, they do so on their own responsibility rather than on the instructions of Defra."