The Natural Environment Research Council (NERC) said it was going ahead with the decision to scrap the centres in Monk's Wood, Cambridgeshire, Winfrith in Dorset and Banchory near Aberdeen. A large number of scientists will be made redundant.
The centres, all part of the Centre for Ecology and Hydrology (CEH), are being closed in a plan to slim the organisation down and save money. The cost-cutting plan itself will cost £43m, and has attracted a huge weight of opposition from the life sciences community in the past few weeks.
Many organisations and research bodies see the work the centres do as uniquely valuable, in areas such as detecting the effects of climate change on the British countryside. More than a thousand hostile responses were received in the consultation exercise about the proposals, with Tories and Liberal Democrats coming together in protest.
Yesterday the NERC brushed all this aside after its 18-strong council confirmed the original closure plan in its main outline. The present nine CEH sites will be reduced to four, with Monk's Wood, Winfrith and Banchory to be closed. Staff from them who are not sacked will have to move to other sites including Wallingford in Oxfordshire, and Edinburgh.
The council said it was responding to the criticism, and amending the plans, by making more funding available. Another £1.3m will be added to the CEH annual budget of £15m, it said, to safeguard the future of essential scientific work, which will be transferred to other CEH stations, and preserve "up to 40" of the 200 research jobs due to be axed.
The concession cut little ice with environmentalists who see the plans as very damaging. "This flawed decision shows how out of touch the NERC council is with biodiversity research and its uses to conservation organisations," said Mark Avery, the conservation director for the Royal Society for the Protection of Birds.
Many other bodies condemned the move. Tom Oliver of the Campaign to Protect Rural England said it was "short-sighted and wrong-headed".
The charity Butterfly Conservation said it was "appalled". The chief executive, Martin Warren, said: "This is not a time for closures. We need more information, not less, about what is happening to our environment and our planet. NERC is unable to grasp this."
One of the main concerns last night was that it is still not clear what research will be carried on elsewhere when the stations are closed, a point which was picked up in criticism from the Royal Society. "While, on the one hand, we are told the work on predicting the impacts of climate change on biodiversity is to be preserved, on the other, work on the prediction of climate change impacts is identified as an area where CEH is planning to do less," said the Royal Society's vice-president Professor David Read.
Last night the NERC's chief executive, Professor Alan Thorpe, said it would be known "in about a month" exactly what science projects would be preserved, after talks with staff. "What we have done is put in place the right shape and size of CEH for the future, with a long-term structure to deliver this science properly," he said.Reuse content