More details of differences between two environmental agencies over Pembroke's £1bn power station have been revealed.
Environment Agency Wales (EA) granted a permit for RWE npower's plant last November despite opposition from the Countryside Council for Wales (CCW).
Friends of the Earth Cymru (FoE) have obtained a copy of CCW's advice raising fears about marine life, although EAW insists it is being protected.
FoE say such concerns could have a low priority under a future merged agency.
The two bodies are due to join forces with the Forestry Commission Wales in April 2013 to form a single agency responsible for environmental issues in Wales.
Planning permission for the gas-fuelled station, which could power up to three million homes once completed, was granted by the UK government in 2009.
The EA said it carried out "extensive" investigations into the potential impact before deciding to issue a permit.
FoE opposed the licence to operate claiming the station would waste heat and damage marine life.
In July the Welsh government asked CCW for more information about its objections, and a response to those objections from the EA.
FoE have now obtained a copy of CCW's detailed objections via a Freedom of Information request.
In it, the CCW stated that it "is unable to agree with the EA's conclusion of no adverse affect on the integrity of Pembrokeshire Marine Special Area of Conservation".
In the document, the CCW warns that the plant would have a damaging impact on habitats and species already under threat, including herring, bass and gobies.
It also claims its case had been misrepresented in the EA's final environmental assessement document.
Gordon James, of Pembrokeshire FoE, said the letter showed "remarkable strong criticism", and claimed the station should have been subject to a public inquiry.
"It's shameful that the Welsh government has ignored the remaining strong objections of its environmental experts to this damaging and wasteful power station," he said.
"This dispute also raises strong concerns about the effectiveness of the body that will emerge from the amalgamation of the Countryside Council for Wales, the Environment Agency in Wales and the Forestry Commission.
"It appears that in a unified body strong objections from the government's environmental scientists will have to quietly acquiesce behind closed doors to the regulatory priorities of the agency."
Mr James added that the European Commission was investigating a complaint from FoE about the Pembroke power station.
Steve Brown, area manager for Environment Agency Wales, said it was the "first sight" they had had of the document, but it did not change their decision to issue a permit.
"This decision was the result of one of the most intensive assessments we have ever carried out in Wales," he said.
"The Pembrokeshire Marine SAC is one of the most important and environmentally sensitive locations in Wales and must be protected by law.
"In issuing this permit, we made sure that the local environment has been protected but at the same time safeguarded energy security and the economic interests of the area."
Dr David Worrall, CCW regional director for west Wales, said: "The Countryside Council for Wales' position has not changed since we started to advise on Pembroke Power Station back in 2004.
"Our concerns remain about the impact of the power station on the Pembrokeshire Marine Special Area of Conservation."