Controversial assessments of disabled people that have led to many losing their state benefits will be reformed, said Steve Webb, the Liberal Democrat work and pensions minister.

He accepted there was genuine anger about how claimants of employment support allowance (ESA) had been treated. The "vast majority" of claimants for ESA, which has replaced incapacity benefit, are deemed fit for work by Atos, the French company which is paid £100m a year to assess claimants.

Yet four out of 10 of those who appeal against the decision by Atos are successful, a process that costs the taxpayer £50m a year. Last month Atos, whose staff assess around 11,000 benefit claimants a week, was savaged by the cross-party work and pensions select committee after it found that many people had "not received the level of service from Atos which they can reasonably expect".

Webb said: "In the past, we accept, that the Department for Work and Pensions (DWP) folk just went 'bang Atos says no'. We are now taking more control of that." The system of "work-related assessments" which Atos carries out on the government's behalf is currently the subject of an independent, state-funded investigation by Professor Malcolm Harrington.

Webb said he had held discussions with his Tory colleague at the DWP, Chris Grayling, over the future role of Atos in assessments and that the government understood that change was needed. He said: "One of the changes Harrington recommended is that you don't just take what the Atos assessor says and tick the box. You say, 'let's see what the consultant says'. If I need more information I will ask for it."

"I am sure there are brilliant Atos inspectors and very poor ones, it is a big organisation, but if someone hasn't done the assessment properly there is much of a safety valve now to say hang on this assessment says no problem but I have got all these reports from the medics.

"The way Chris put it, is the contribution of the Atos judgment to the decision will be a smaller part. And that has got to help."

On Sunday Lib-Dem delegates at their Birmingham conference endorsed calls for Atos's "tick box" system of medical tests to be replaced by something more accurate and less stressful for those who go through it