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GB Energy chairman will be based in Manchester
The government said it would be led by the “talent and skills of the working people in the Granite City”.
Scottish Conservative energy spokesman Douglas Lumsden said it was “an insult” to the north east of Scotland that the chairman would be based hundreds of miles away.
“Common sense should have told Keir Starmer that the person running one of his flagship policies should be on the ground in Aberdeen,” he said.
“Instead, this decision sums up how disconnected Labour are from the needs of these communities.”
Aberdeen is already home to much of the UK’s oil and gas and offshore wind industries.
Energy security secretary Ed Miliband said the company would help make Britain a “clean-energy superpower” by 2030.
A department for Energy Security spokesperson said GB Energy would be headquartered in Aberdeen to recognise the “expertise, skilled workforce and diversity of projects already in place”.
They added: “The chair and board will also regularly spend time in the city, including with the local community and businesses.”
The government pledged to invest £8.3bn into the company over the course of this parliament, which is expected to be raised through a windfall tax on oil and gas firms.
Labour previously said it would not issue new oil and gas licences, but has also said it would not overturn existing permits.