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By Chris Mason & Henry Zeffman
BBC News
The energy secretary questioned the decision to approve a controversial power plant in the constituency of a cabinet colleague.
Claire Coutinho's department admitted she had sought "clarification" on the process that led to the waste-burning incinerator being signed off.
But it denied a claim in leaked legal advice that she had wanted to overturn approval of the scheme.
The project is opposed by Environment Secretary Steve Barclay, the local MP.
MVV Environment, a German energy company, wants to build the plant in Wisbech, in Mr Barclay's North East Cambridgeshire constituency.
It would be one of Europe's biggest waste-to-energy incinerators, burning non-recyclable waste in order to generate energy for local industrial use.
An internal legal note compiled after consultation with the government's most senior legal adviser, Sir James Eadie KC, stated that Ms Coutinho had "sought to overturn" a junior minister's decision to approve the incinerator.
It warned that her intervention, among other factors, risked any decision to block the scheme being deemed unlawful by the courts.
Ms Coutinho's department insists that she never sought to overturn the scheme, and that she only wanted to ensure "the decision-making process had been properly followed".
She then concluded that the process was correct, and upheld the approval decision.
The scheme was given the go-ahead last month by Ms Coutinho's Department for Energy Security and Net Zero (Desnez), following a recommendation from the Planning Inspectorate.
Sources claim Mr Barclay was livid at this decision, and sufficiently angry that Downing Street was aware of his fury.
Announcement taken down
The decision was taken by Lord Callanan, a junior energy minister, while Ms Coutinho was out of the country.
Upon her return, she is understood to have raised questions about why the matter had been delegated to Lord Callanan and whether that had been appropriate.
The day after Lord Callanan's approval of the scheme was confirmed, the announcement was suddenly removed from the internet. It was later reinstated.
To move ahead, the scheme also requires a permit from the Environment Agency (EA), a public body sponsored by Mr Barclay's environment department.
The BBC revealed last week that concerns about Mr Barclay's relationship to the case had been raised by civil servants.
This prompted discussions with Whitehall's propriety and ethics unit, with Mr Barclay agreeing to delegate that decision to a junior minister in his department, Mark Spencer.
'Perception of bias'
The leaked legal advice offers a view on what it calls "the proposal for an urgent direction to the EA to pause permitting applications for up to a year".
But it concludes that this "would be unlawful because the consultation undertaken with the EA was plainly inadequate", describing Mr Barclay's longstanding public opposition to the scheme as a "powerful exacerbating feature given the perception of bias".
As part of the "factual background" to the case, the legal advice states: "It will not escape the notice of potential challengers or the courts that… there were issues with [the approval] in which [Ms Coutinho] sought to overturn the decision by the minister in Desnez, Lord Callanan.
"The strong impression is, and the allegation in litigation will undoubtedly be, of every possible step being taken to overturn the effect of a [decision] on grounds of political advantage, rather than on legitimate policy grounds."
A Desnez spokesperson said: "Clarification was sought on whether the decision-making process had been properly followed, rather than to overturn any decision.
"Ultimately, it was agreed that it had, and the relevant documentation was reinstated on the website."