Scotland’s control over its oil and gas reserves could be hampered by a regulatory power grab by the European Commission, a Scottish MEP has warned.

Tory MEP Ian Duncan claims that the European Commission’s tasking of a private company to create an EU-wide best practice “reference document” (BREF) to set environmental and health and safety guidelines for the onshore and offshore industry could be an attempt to impose a Europe-wide ban on fracking “by the back door”.

A wider row with Brussels now looms as Duncan’s protest was backed last week by the Holyrood and Westminster Governments as well as the industry body Oil & Gas (O&GUK).

A spokesman for the Scottish Government, which remains neutral on fracking pending further investigation, told the Sunday Herald that it was “disappointed that the Commission has signed the contract for the BREF without any prior consultation. We remain sceptical as to how necessary a BREF is for the hydrocarbon industry at this time.”

Dr Duncan, a former petroleum geologist and a member of the European Parliament’s energy committee, also warned of added costs to Scotland’s existing offshore industry at a time when the industry is struggling to weather the oil price crash.

Last week an O&GUK report calculated that 65,000 jobs have been lost in Britain’s offshore oil sector since the start of last year. The industry body also warned that oil and gas firms could slash investment in the North Sea by more than £10 billion annually over the next three years after incurring their worst cash flow deficit since 1976 due to plummeting oil prices

“The collateral damage from this BREF could be enormous and will knock confidence in Scotland’s oil and gas industry,” Duncan told the Sunday Herald.

A spokeswoman for O&GUK said that the new hydrocarbon BREF had “caught the industry by surprise” and that the process of monitoring compliance would “take up a lot of time for the all companies involved in conventional and unconventional oil and gas extraction”.

“A bad outcome would be more regulation which is duplicative and unnecessary and the extra costs this would impose on the industry,” she said.

In May the new Juncker Commission awarded a contract to the London-based engineering and project management consultancy Amec Foster Wheeler to produce the BREF on the exploration and extraction of hydrocarbons.

The Commission justifies getting involved in the regulation of shale gas activities by saying that the new techniques of hydraulic fracturing, “trigger concerns about public health and environmental effects”, pointing to the risk of contamination of ground and surface water.

Last week EU Environment Commissioner Karmenu Vella said in response to a written parliamentary question from Ian Duncan that the purpose of the BREF “is not to restrict fossil fuel extraction, but rather to set out a level, predictable and transparent playing field for oil and gas activities as well as to help address public concerns for domestic oil and gas production”.

But the MEP said that the UK had set the “gold standard” for environmental and health and safety standards in the extractive industries and questioned the need for extra regulation.

He also queried the legal basis for the rules, branding the Commission’s intervention “profoundly anti-democratic”. Neither the European Parliament nor member states were consulted before the BREF was put out to tender and Westminster and Holyrood will have no oversight function.

The Commission has claimed that the lack of legal basis was “not an obstacle for the development of a BREF facilitating the identification of best available techniques”.

O&GUK says that previous BREFs, including a 2006 BREF on large combustion plants, had been created on the understanding that recommendations would be voluntary, but that these had later become legally binding.

Mick Borwell, O&GUK’s environmental director, said: “The Commission has still not outlined the scope, objective and legal basis of the Hydrocarbons BREF. The regulatory uncertainty of the BREF poses a significant business risk to companies with an interest in the North Sea and the goal of maximising economic recovery from the UK Continental Shelf.

“We have asked the UK Government to make clear to the Commission that the offshore industry should not be included within the scope of the BREF since it poses a significant threat to maximising economic recovery of known conventional offshore resources without offering reciprocal benefits.”

A spokesman for the UK Government’s Department of Energy and Climate Change said it would be working with the European Commission to ensure that any regulations do not contain “unnecessary red tape”.

“We have also made our position very clear on shale gas, which we believe is a fantastic opportunity for the UK, for energy security and jobs, and we are keen to get the industry moving.”

In January the Scottish Government imposed an indefinite moratorium on onshore fracking to allow for public consultation on the controversial drilling technique – which involves pumping water and chemicals at high pressure below ground to fracture shale rock and release gas – and more research into its impact on public health.

The moratorium led Ineos, the Swiss owners of the loss-making Grangemouth petrochemical plant, to put on hold £640 million plans to use fracking from nearby sites to produce gas for the terminal.

Richard Dixon of green lobbyist group Friends of the Earth Scotland said: “Industry always squeals when anyone talks about firmer regulation but this is a perfectly sensible effort to make sure the oil and gas industry is meeting the highest standards.

"In the North Sea this is needed as we move into a phase of smaller operators using ageing equipment to squeeze the last out of tired reserves. For unconventional gas this is needed because the Scottish Environment Protection Agency have already said that current regulations cannot adequately control this new industry. If the industry is already as good as they like to claim they should have no fear of a review which simply defines best practice.

"Any talk of a backdoor route to banning fracking is pure fantasy, especially since the European Commission have been clearly on the side of industry from the start."