They say financial rules for nuclear operators include subsidies that have not been approved by the commission.
These include capping of liability for accidents, which they say at least halves the cost of nuclear electricity.
The government says it is confident that policies do not provide subsidies.
The complaint, by the Energy Fair group, also says that the UK’s carbon floor price and feed-in tarriffs amount to state aid for the nuclear industry.
State coffers would also have to meet cost overruns on nuclear waste disposal, they argue.
Dorte Fouquet of the German legal firm BBH, who drew up the complaint, said that EU energy policy was based on having an open market with a level playing field.
“The commission has repeatedly underlined that distortion of the market is to a large extent caused by subsidies to the incumbents in the energy sector,” she said.
“This complaint aims to shed some light on the recent shift in the energy policy of the United Kingdom where strong signals point to yet another set of subsidies to the nuclear power plant operators.”
Last year, a committee of UK MPs also said that the government was subsidising nuclear power, despite promises that it would not.
It sees the construction of about eight new reactors within a decade as essential for meeting climate change and energy security goals.