Sir Muir Russell walked away with nearly £6000 a month for leading a probe which cleared scientists at the University of East Anglia of data manipulation.
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Russell was the Scottish Executive’s permanent secretary at the time of the botched plan to construct a world-class building to house MSPs.
The project’s cost jumped from £40 million to nearly £430m and cast a shadow over devolution.
An inquiry into the fiasco criticised the decisions of civil servants who were responsible for the plan.
Lord Fraser, who chaired the probe, said of the mandarin: “Clearly the top man was Sir Muir Russell.
“There were a number of very sharp criticisms made of him in the Scottish Parliament, and I respectfully adopt their recommendations.”
Russell’s colleagues were also accused of not passing on the full cost estimates to the late First Minister Donald Dewar, whose spell in office was dogged by the row over the building’s soaring price tag.
The civil servant left his £160,000 post in 2003, accepted an early retirement package, and then resurfaced as the principal of Glasgow University on a salary and pension deal of more than £200,000.
He left this job last year, but has since held various part-time roles. One berth has been to chair the Independent Climate Change Email Review, set up last December.
The inquiry investigated claims that researchers at East Anglia had distorted statistics on global warming.
Hacked e-mails written by university staff led to fears that information on climate change was being manipulated, a row that was played out internationally.
The six-month probe concluded with Russell and his team noting the “rigour and honesty” of the scientists.
A freedom of information request has revealed that the university paid Russell a £40,000 fee for his chairmanship.
He also benefited from £2908 in travel and £976 for accommodation.
The Review website notes that the team met on 15 occasions, which works out as the equivalent of Russell receiving £2666 per meeting.
John Wilson, an SNP MSP in Central Scotland, said: “It is difficult to accept that Muir Russell should have received £40,000 for an inquiry conducted by East Anglia university.
“On top of pension payments and an early-retirement package, he is now making more money ultimately at the expense of the public purse.”
Lothians MSP Margo MacDonald said Russell “always seems to land on his feet”, and added, “He’s especially lucky since he has escaped from the failure of controlling costs on the Holyrood project.”
A spokesman for East Anglia University said: “We agreed a fixed fee in advance with Sir Muir.”
Attempts were made by the Sunday Herald to contact Russell, but he could not be reached.