The 2,000MW combined cycle gas turbine (CCGT) in Wales, which was developed by RWE at a cost of £1 billion, was officially opened in September 2012.
However, the EC says that the use of the cooling system, which returns the “warm water with a heavy biocide load” into the protected Milford Haven waterway, breaches environmental standards.
In its “reasoned opinion” sent to the UK, the commission stated “it does not appear to have been the case” that all the potential environmental impacts were assessed.
The EC claimed the development and construction consents, as well as a water abstraction licence and a permit for the dredging the cooling system intake and outflow, were granted “before the full environmental assessments were completed”.
In a statement, RWE Generation UK said “this is a matter for the UK Government” but that is would continue to provide any information as required.
The statement added that planning consent was granted in February 2009 “after a thorough and robust determination process”.
“In November 2011, the Environment Agency granted an Environmental Permit for the operation of the power station having fully considered its potential impacts and concluding that it will have no significant impact on the local environment.
“Since then, no legal action has been brought against RWE or Pembroke Power Station and we are continuing to operate the plant in accordance with the strict conditions set out in our Environmental Permit.”
Ceri Davies, director for knowledge, strategy and planning for Natural Resources Wales, said: “We have been expecting the Commission’s latest opinion on these matters.
“We will now fully consider these in order to submit evidence and advice to the Welsh and UK Governments to help with their responses.”
A spokesperson from the Department of Energy and Climate Change added: “We are carefully considering the reasoned opinion and will be deciding on the appropriate action to take in due course.”