The closure of landfill sites is causing increased outbreaks of fires and odour problems at waste treatment facilities, according to a report from the Environmental Protection Agency.
In its report on waste enforcement, the EPA said that there has been nearly a tenfold increase in waste being stored for export in just four years to 2014.
There were six fires that year, including an "extensive" outbreak at an Oxigen facility in Ballymount, west Dublin.
Complaints about odours made up over 90% of the complaints received by the EPA about waste facilities.
The authority said non-hazardous waste transfer facilities accounted for a disproportionate number of complaints - the sector had a third of waste disposal licences but accounted for 70% of complaints.
Three waste companies were taken to the courts in 2014 for breaches of regulations, with Oxigen receiving a conviction and ordered to pay €10,000.
Two other companies received the Probation Act and ordered to pay a total of €29,000.
Programme Manager with the EPA Mary Gurrie said waste companies need to operate their facilities better.
She said: "Inspections conducted by the EPA have found poor management and storage of waste at some facilities which is leading to unacceptable odour nuisance and an increased risk of fires.
"The EPA is targeting our enforcement at facilities that pose a risk to the environment and public health and will continue to take action against companies and their directors to ensure compliance."
Around 560,000 tonnes of waste were exported abroad to be converted into fuel through incineration.
The number of landfills available decreased to just six in 2014 compared, to 20 in 2011.
The report noted that eight shipments of waste - comprising 400 tonnes - were returned to Ireland after they were found to be in breach of regulations and stated that this trend had to be reversed.
Dublin's Poolbeg Incinerator, which has the capacity to take 600,000 tonnes of waste a year, is due to open in 2017.