John Beddington also said the impact of global warming has been exaggerated by some scientists.
Another top British scientist Mike Hulme raised questions whether Pachauri of India should continue to head the Intergovernmental Panel on Climate Change.
In the wake of an admission by IPCC that it grossly overstated the rate at which Himalayan glaciers were receding, Beddington told The Times that climate scientists should be less hostile to sceptics who questioned man-made global warming.
He also condemned scientists who refused to publish the data underpinning their reports. Beddington said that public confidence in climate science would be improved if there were more openness about its uncertainties, even if that meant admitting that sceptics had been right on some hotly-disputed issues.
Pachauri's 'voodoo science' remark to slam India's Environment ministry over the Himalayan glacier issue drew more flak from another scientist. Hulme, Professor of Climate Change at the University of East Anglia, criticised Pachauri for his dismissive response last November to research by an Indian group suggesting that the UN body had overstated the threat to the glaciers. Pachauri described it as 'voodoo science'.
"Pachauris choice of words has not been good. The question of whether he is the right person to lead the IPCC is for the 193 countries who make up its governing body. Its a political decision." Prof Hulme said.
Beddington said that the false claim in the IPCCs 2007 report that the glaciers would disappear by 2035 had exposed a wider problem with the way that some evidence was presented.
"I dont think its healthy to dismiss proper scepticism. Science grows and improves in the light of criticism. There is a fundamental uncertainty about climate change prediction that cant be changed," said.
"Certain unqualified statements have been unfortunate. We have a problem in communicating uncertainty. Theres definitely an issue there. If there wasnt, there wouldnt be the level of scepticism. All of these predictions have to be caveated by saying, Theres a level of uncertainty about that."
Beddington said that particular caution was needed when communicating predictions about climate change made with the help of computer models.
"Its unchallengeable that Carbon Dioxide traps heat and warms the Earth and that burning fossil fuels shoves billions of tonnes of Carbon Dioxide into the atmosphere.
"But where you can get challenges is on the speed of change. When you get into large-scale climate modelling there are quite substantial uncertainties.
"On the rate of change and the local effects, there are uncertainties both in terms of empirical evidence and the climate models themselves."
He said that it was wrong for scientists to refuse to disclose their data to their critics: "I think, wherever possible, we should try to ensure there is openness and that source material is available for the whole scientific community."
"There is a danger that people can manipulate the data, but the benefits from being open far outweigh that danger", he added.
Pachauri on the report's mistakes, glacier melting
India inches closer to UN Security Council seat
Pachauri accused of making a 'fortune'
Pachauri wont resign over erroneous IPCC report
Impartial probe into Sri Lanka war critical: UN