An Taisce yesterday lodged an appeal against plans to build a toxic waste-burner in Ringaskiddy on Cork harbour and a waste-burner near Duleek in Co Meath.
The environment group has health and safety concerns about the controversial incinerator, and about emergency evacuation plans and pollution risks.
The EPA gave the go-ahead for the Ringaskiddy plant and the Co Meath facility last month after planning permission was secured.
Mr Ian Lumley, an An Taisce spokesman, claimed yesterday that the EPA had failed to obey a series of rules imposed by planners.
"We are seriously concerned that there is no independent review procedure on EPA decisions," he said, claiming that the authorities had yet to address 14 issues raised by planning inspectors.
Both projects have met with significant opposition from politicians and residents' groups who mounted major protest campaigns on health and environmental grounds.
Locals in Ringaskiddy are also concerned over the threat a major flood could pose to the incinerator.
The proposed site was swamped by several feet of water after storms battered the south coast in late October.
An Taisce said it would raise this matter and waterlogging at the site with the EPA.
Mr Lumley said they were concerned over an EPA requirement to raise the emission stack at the Duleek plant by 25 metres, to more than 60 metres.
Officials said it contradicted conditions attached to planning rights granted on the basis there would be no impact on the Boyne World Heritage Site.
If allowed, the incinerator would be visible from one of the megalithic passage tombs at Dowth, Newgrange, inside the Unesco-designated World Heritage Site.
The Ringaskiddy plant, with an initial cost of €75 million, will handle 100,000 tonnes of hazardous and non-hazardous waste a year.
The plant, which could be operational in 2007, is likely to employ some 50 people.
The Duleek site will deal with 150,000 tonnes of non-hazardous rubbish at a cost of €85 million.