The council failed to report problems with landfill gas and leachate at the site.
EPA regional manager for the north-east Renee Palmer said the management responsibilities for a landfill continued long after it had been closed.
"Landfill gas and leachate are normal issues with any landfill, even long after it has been closed and covered, and EPA uses licensing and post closure pollution abatement notices to apply conditions that the operator must meet for the protection of the environment and public health.
"In this case, the council failed to report to EPA that the landfill was not compliant with licence limits on those emissions.
"Leachate and landfill gas must be properly managed to prevent them from affecting ground or surface water and causing problems with odour.
"When the licence holder fails to notify EPA of a non-compliance, it hinders the authority’s ability to require that licence holder to take action to fix the problem,” Ms Palmer said.
EPA will continue to work with the council to monitor the site. The council has employed a waste management officer who is tasked with managing the former landfill.
Strathbogie Shire Council has the right to appeal the decision.
Council acting chief executive Phil Howard said "limited resources and administration" contributed to the breach.
"Landfill gas and leachate are normal issues with any landfill; however council failed to uphold the Environmental Protection Authority’s reporting requirements under our licence agreement," Mr Howard said.
"We have recently appointed a new Waste Management Officer to fill the position of an outgoing Waste Management Officer.
"This role involves overseeing waste management and practices at transfer stations, waste collection points, regional waste groups, assisting with projects and operations and reporting to statutory, governing, and regulatory authorities.
"Council apologises to our ratepayers for receiving a fine from the EPA and will work with the EPA to ensure we meet our obligations at the Violet Town landfill moving forward.
"Council meets regularly with Regional EPA staff and we look forward to working through these issues with them," he said.
