Britain’s planned nuclear reactor programme could be delayed for years, and the nation’s long-term energy policy thrown into turmoil, as European commission officials launch the first stage of a formal investigation into the use of taxpayer subsidies to support the development.

Sources in Brussels have indicated that Britain hopes to win approval for a multibillion-pound deal with French energy giant EDF at the initial stage, which usually takes two months.

But if after a preliminary investigation the EC’s competition directorate decides to launch a full-scale investigation, that would last at least 18 months and probably two years or more. Such an outcome is made more likely by reports that ministers and EDF are discussing a minimum or “strike” price for the nuclear-generated electricity of a little under £100 per megawatt hour – nearly double the current market rate. However ministers will be hoping that their regular meetings with EC officials will make it more likely that a full inquiry will be avoided.

Under the proposals, a nuclear power station – the first for a generation – will be built at Hinkley in Somerset, and the government will guarantee a minimum price for the electricity produced for 30-40 years, a deal which could cost customers a billion pounds a year or more.

News of the latest obstacle to the nuclear building programme comes before the expected announcement next week by the energy secretary, Ed Davey, of whether EDF has won planning permission for the 3.2 gigawatt Hinkley nuclear plant. He is widely expected to give the scheme the go-ahead.

Expectations are rising that Davey could also announce some details of the new contract, including the strike price, in what would be a useful counter to critics that the coalition is not doing enough to stimulate investment to boost the economy and tackle the UK’s threatened energy shortages.

A delay imposed by Brussels would cast new doubt on the £14bn project as it would be likely to make it harder for EDF to raise the capital needed until its contract with the government was fully approved. That in turn would delay the entire nuclear build programme, under which the government wanted 16 gigawatts of new nuclear power operating by the middle of the next decade.

“The government wouldn’t need state aid approval for nuclear if it wasn’t trying to subsidise a risky technology that could wind up costing more than the renewable alternative,” said Doug Parr, policy director for the anti-nuclear campaign group Greenpeace.

Maria Madrid, spokeswoman for Joaquín Almunia of Spain, the European commission vice-president in charge of competition, told the Guardian: “The commission is in contact with the UK authorities on this issue, but has not received a formal notification so far. We are discussing this issue. It’s confidential. We never communicate on preliminary discussions.”