Britain’s ability to respond to security threats could be undermined if the Ministry of Defence significantly cuts its funding for research, the government’s chief scientific officer has warned.

In a letter to John Hutton, the defence secretary, John Beddington said he was “greatly concerned” to have heard “from several sources” that the MoD was considering significant cuts in its research funding.

Such cuts would be “sharply at odds” with the prime minister’s recent
commitment to sustaining the level of research investment through the current economic difficulties, said Prof Beddington.

He warned he was particularly concerned about the potential impact of any cuts on the MoD’s engineering facility, the Defence Science and Technology Laboratory. As well as being core to a wide range of MoD requirements, DSTL also provides cross-government capabilities, including the biological capabilities of Porton Down.

“The cross-government counter-terrorism R&D programme depends critically on particular DSTL capabilities which, if undermined, might seriously reduce our ability to respond to future threats and conflicts,” said Prof Beddington.

He said another concern was the potential withdrawal of MoD funding from the integrated climate programme, an inter-departmental research collaboration. This would cause “substantial damage” to Britain’s ability to deliver earth system modelling that is “of key importance to achieving our climate change goals”. The letter, a copy of which has been obtained by the Financial Times, was sent to Mr Hutton last month and copied to, among others, Jacqui Smith, the home secretary, and Ed Miliband, the climate change and energy secretary.

It comes as the MoD finalises its finances for the coming year. The department, which has been struggling to balance the demands of operations in Iraq and Afghanistan with a tight budget, has been seeking to make savings.

Mike Clancy, deputy general secretary of the Prospect union, said he was not surprised by the prospect of cuts in R&D funding given the pressure on overall defence expenditure. It would also be easier for the department to avoid scrutiny if it cut R&D expenditure rather than particular programmes, he added.

It is understood that Mr Hutton has responded to Prof Beddington. MoD sources said any decisions to cut funding would not be taken lightly but the department had to weigh up whether its resources were spent on buying equipment such as more tanks for the armed forces or on targeting issues such as climate change.

“The chances are any decisions will always come down in favour of equipment and providing defence capabilities,” said one MoD source.

The MoD declined to comment on the letter but said: “We are aware of how important research is to future capability, which is why the department’s research and development spend is more than £2bn a year.

“Whatever action is taken on the programme, the overwhelming proportion of this spend will be unaffected.”

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