Big energy companies hampered plans to protect porpoises off the north east of Scotland by forcefully lobbying the Scottish Government behind the scenes, according to internal documents obtained by the Sunday Herald.

Confidential correspondence released under freedom of information law reveals that the Scottish company SSE and Spain-based EDP Renewables warned ministers that a planned conservation area for harbour porpoises could kill their plans for large offshore wind farms in the Moray Firth.

The companies cautioned privately that delays and tougher environmental restrictions could cause shareholders and investors to pull out. They disputed that porpoises needed the protection, highlighted the risk of legal action and threatened to demand compensation.

In the wake of intense pressure, the Scottish Government decided to ditch the porpoise conservation area in the Moray Firth. It has instead proposed a large area off the west coast, where no wind farms are currently planned.

The revelations have infuriated wildlife groups, who accuse ministers of giving energy companies preferential treatment. Official claims that all sides had been dealt with “equitably” were not true, they say.

From June to November last year the companies had almost weekly conference calls with government officials. They received detailed briefings on timetables and processes, were kept abreast of what ministers were thinking and were given confidential draft science reports.

The first meeting granted to environmental groups on porpoise conservation areas took place on November 2 2015. By that time the decision to abandon plans to designate an area in the Moray Firth had virtually been made.

Perth-based SSE leads a £2.6 billion offshore wind project in the outer Moray Firth, backed by private investors from Denmark and a Chinese state corporation. Next year contractors are due to start erecting 84 giant turbines out at sea expected to produce enough power for 450,000 homes by 2019.

Madrid-based EDP Renewables leads another, larger, scheme for an adjacent area of the outer Moray Firth. It is planning to build between 189 and 339 turbines to generate enough electricity for 700,000 households.

Plans for a Special Area of Conservation (SAC) for harbour porpoises in the Moray Firth were put forward by the Scottish Government’s wildlife advisers in 2015. This followed a threat of legal action by the European Commission, which was concerned at the UK’s failure to protect the animals.

The seas around Scotland and the rest of the UK host some of the highest numbers of harbour porpoises in Europe. But conservationists are worried that numbers have been declining because of pressures from the fishing industry and pollution.

The suggested SAC for the Moray Firth overlapped the two proposed wind farms, and rang alarm bells within SSE and EDP Renewables. The companies were worried that the protocols they had agreed to protect marine mammals while pile-driving turbine foundations into the seabed would have to be rewritten.

The released correspondence shows that both companies wrote twice to the then energy minister, Fergus Ewing, complaining about the planned SAC. In July 2015 SSE said it was “extremely concerned”, and in August it warned of “a risk of default and contract termination.”

In November EDP warned the minister of “legal and scientific flaws”. Launching a formal consultation on the SAC would be “premature due to the lack of a sound legal footing and robust scientific data”, it said.

An unnamed senior official from SSE also had lunch in the Scottish Parliament with the then environment minister, Richard Lochhead, in September 2015. Ewing and Lochhead both reassured the industry that they would take a “pragmatic and efficient approach”.

After the two companies were given internal reports by government advisers, they conducted detailed reviews of the legal and scientific basis for the SAC. SSE’s analysis concluded that the science was “superficial”, “flawed” and biased against the renewables industry.

EDP alleged that there were “considerable flaws” in the data and the case for the SAC was “not legally robust”. The outer Moray Forth was “no hotspot for harbour porpoise”, it said.

In December, ministers told the companies that they had decided not to proceed with the Moray Firth SAC. Earlier this year, the government’s wildlife agency, Scottish Natural Heritage, held a consultation into another harbour porpoise SAC covering the Minches and the Inner Hebrides.

The whole procedure has angered Whale and Dolphin Conservation, the group that has been leading efforts to increase protection for harbour porpoises. “The industry was successful in derailing the process,” said the group’s senior policy manager, Sarah Dolman.

“We are appalled that the Scottish Government’s stakeholder engagement was so one sided, including sharing key documents with wind farm developers but not with the conservation community.”

Dolman argued that it was possible to reduce climate pollution by building wind farms at the same time as protecting porpoises. “Yet government has allowed industry to strip porpoises of necessary protection in the Moray Firth,” she said.

Aedán Smith, head of planning for the environmental organisation Royal Society for the Protection of Birds in Scotland, called for processes to be open and fair. “Any suggestion that additional opportunities may be have been provided for developers to influence the process unfairly is a serious concern and needs to be thoroughly reviewed as soon as possible,” he said.

Both SSE and EDP Renewables stressed that they took their environmental responsibilities very seriously. They said the science behind the Moray Firth SAC had “serious deficiencies” and relied on “limited, elderly and patchy data”.

SSE’s senior project manager, Steven Wilson argued that harbour porpoise populations would not be “significantly affected” by wind farm operations. “We engaged, as any responsible developer would do, with all relevant parties, over many years, to deliver an approach that minimises the impact on any species,” he said.

“Our aim throughout our engagement with government and stakeholders was to seek clarity about the scientific basis and timescales associated with the SAC process, and how we could contribute to it in order to fulfil our environmental obligations.”

Dan Finch, the project director for EDP Renewables, alleged that insufficient data on harbour porpoises had been “heavily manipulated”. Like other developers, the company had contacted the Scottish Government to express its concerns, he said.

He insisted that the wind farms would not have a “significant effect” on porpoise populations. “This was reviewed on our behalf by highly respected experts who raised material concerns regarding the robustness of the modelling approach,” he said.

The Scottish Government pointed out that harbour porpoises were a protected species in all European waters. The scientific case for the Moray Firth SAC “did not meet the standard of evidence required,” a government spokeswoman told the Sunday Herald.

“Fundamental errors were identified in the site population estimates, survey data, and the application of expert judgement was flawed. Marine Scotland has been taking forward discussions with stakeholders around harbour porpoises.”