Britain’s nuclear clean-up agency has begun a review of its pay structure after The Times revealed that public servants were being paid millions of pounds in “guaranteed” taxpayer-funded bonuses every year.

Stephen Henwood, chairman of the Nuclear Decommissioning Authority (NDA), whose clean-up activities at 19 nuclear sites, including Sellafield, absorbed £1.6 billion of public money last year, said that the system needed to be reformed.

He said that four non-executive NDA directors were conducting a detailed review of the bonus scheme, under which some staff members have been asked to maintain a “tidy desk policy” as a criterion for payment. “I think there is room for improvement,” he said. “There is scope for a more direct link to performance.”

The Times revealed in April that the NDA paid nearly £3.8 million in bonuses last year to its 315 staff. The figures, obtained under the Freedom of Information Act, also showed that all of the NDA’s regular workers received a bonus in both 2008 and 2007.

The payments, which ranged from an average of just under £12,000 to nearly £37,000, were made on top of regular salary payments totalling £19.5 million.

Fresh details of the pay deal will be unveiled on Monday in the NDA’s annual accounts.

Since its formation in 2005, the NDA, which consumes around half of the Department of Energy and Climate Change’s £3 billion budget, has struggled to recruit and retain staff.

It took the Sellafield-based organisation a year to recruit a new chief executive, Tony Fountain, after the departure of his predecessor, Sir Ian Roxburgh. Mr Fountain, whose appointment was announced last month, takes up his position in October. He will join the NDA from BP, where he was chief operating officer of its Fuels Value Chains business.

Mr Henwood said that the review of the bonus scheme was being led by Jim McLaughlin, director of human resources, who joined last year from Royal Bank of Scotland. He is working with David Illingworth, chairman of the NDA’s audit committee, and three other non-executives.

Matthew Elliott, chief executive of the TaxPayers’ Alliance, the campaigning group, said: “It is good news that the NDA is planning to reform this severely flawed bonus system. Handing out millions of pounds with apparently no consideration for performance or wider economic conditions is unjustified and wasteful.”

Although 58 per cent of its £2.78 billion budget comes from taxpayers, the NDA is technically a “non-departmental public body”, a type of quango, rather than a regular arm of the Civil Service.

This arm’s-length relationship precludes it from the pay restrictions imposed on regular government departments.

The NDA’s report will also contain fresh estimates of the cost of cleaning up Britain’s contaminated nuclear sites, last put at £70 billion.

The bulk of the NDA’s budget is used to pay subcontractor firms, which employed 18,467 staff on its sites last year. Its budget for the three years to 2011 is £8.5 billion. The clean-up of nuclear facilities has been paid for with a mix of funds.

The NDA’s commercial income, the bulk of which comes from reprocessing spent nuclear fuel at Sellafield, as well as the sale of electricity from the NDA’s two remaining operational power stations at Wylfa and Oldbury, has fallen short of expectations in recent years.

Gone fission

— The Nuclear Decommissioning Authority is a non-departmental public body, established under the Energy Act 2004

— It is responsible for the decommissioning and clean-up of Britain’s civil public-sector nuclear sites

— The NDA is responsible for developing UK-wide strategy for nuclear low-level waste; long-term management arrangements for higher radioactive waste; and the clean-up of 19 former UKAEA and BNFL sites run by British Nuclear Fuels and the UK Atomic Energy Authority

— Its 2009-10 annual budget of £2.78 billion comprises £1.63 billion in government “grant in aid” and £1.15 billion in project income

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