Half of legal actions taken by the EPA in 2013 were against waste operators - despite waste licenses only representing 15% of EPA licences.
A report by the Environmental Protection Agency says more than 90% of complaints it received about waste facilities were related to odour.
The 2013 report says the EPA carried out 275 inspections at waste facilities. There were six prosecutions, with fines and costs totalling €86,000.
The organisation says standards of operation and storage at waste facilities must improve, to minimise odour nuisance and fire hazard.
It is also calling for better coordination of local authority enforcement of the waste sector, adding that movement, processing and export of waste have all increased.
Mr Jim Moriarty, manager of EPA’s Office of Environmental Enforcement said, “there is no excuse for poor performance. Under the conditions of their licence waste operators are not permitted to exceed waste tonnage limits and must ensure that the necessary infrastructure to prevent odour nuisance is in place and operating correctly.
"There have been a number of fires also at waste facilities in recent years, and improved practices must be implemented to minimise fire hazards,” he added.
