The Environmental Protection Agency (EPA) has published a list of the nine worst offenders in pollution control at EPA licenced facilities.
The group found five of the nine are food processors - two of which are dairy groups Glanbia and LacPatrick.
The others on the list are Rosdarra Meats, Western Brand Group chicken processors and Arrow Group pig meat processes.
The first three named on the list are members of Bord Bia "Origin Green" sustainability food product and labeling system.
Five of the nine sites are from the agri-food sector.
Source: EPA
The main compliance issues are causing odour and noise nuisance and failing to properly manage wastewater discharges.
Three sites are from the waste sector- the main issues here are poor waste management practices on site and causing odour.
While the nine sites overall accounted for 43% of all complaints received in this period.
An Taisce says the list "again shows" that Irish food processing companies continue to be lead category of EPA licence breaches.
Ian Lumley, An Taisce's advocacy officer, says: "This puts into question to credibility of the sustainability labeling of Irish food processors by Bord Bia.
"Appearance on an EPA worst offenders list should be incompatible with retaining a green label branding".
"This issue comes on top of the increasing climate impact caused by Irish agricultural emissions, which combined with declining biodiversity an high status waters is placing Irish agriculture and food processing in irreconcilable environmental conflict."