Prof Malcolm Harrington, the government appointed adviser on testing welfare claimants, admitted the work fitness test was “patchy”.
He said that as a result of the flaws in the 13 week assessment, which tests physical fitness as well as mental skills, some claimants who were genuinely unable to work, have suffered.
He made the comments during an investigation into the system, introduced by the last Labour government, by the BBC’s Panorama programme.
“There are certainly areas where it’s still not working and I am sorry there are people going through a system which I think still needs improvement,” he said.
The programme, which airs on Monday night, features the story of one man who suffered from heart failure and died 39 days after being declared fit for work.
Stephen Hill was sent to his first Work Capability Assessment in 2010 when he gave up his job as a sandwich delivery man after being referred for tests on his heart.
His wife Denise, who was with him at the assessment, said: “She checked him out. She did his blood pressure and his heart and said to see a doctor as soon as possible.”
Despite the assessor telling Mr Hill to seek urgent medical advice, he was still found fit for work. In the meantime doctors had diagnosed him with heart failure.
He won his appeal but he was ordered to attend another assessment.
“He got a letter for another medical and I couldn’t believe it,” said Mrs Hill. “He’d got to go for a medical when he was waiting for a heart operation.”
But he was again declared fit for work, with the assessor declaring: “Significant disability due to cardiovascular problems seems unlikely.”
Mr Hill died of a heart attack five weeks later.
The assessments are carried out by Atos Healthcare on behalf of the Department of Work and Pensions (DWP).
According to the programme, two and a half million people in the UK take the test because they are too illl to work.
But more than 176,000 cases go to appeal tribunals each year, costing the taxpayer an additional £50 million, a programme spokesman said.
In a statement Atos said staff “carry out thousands of assessments every month in accordance with detailed guidelines as set by the Department of Work and Pensions”.
Previously more than 2.6 million claimed Incapacity Benefit, at a cost of £12 billion a year to the taxpayer.
But in an attempt to make the replacement scheme more rigorous, applicants now undergo the WCA, which can require them to undergo a face-to-face medical assessment and provide a report from their doctor.
But government figures have shown that more than nine out of 10 people who claimed the new sickness benefit have been deemed fit enough to work.
More than a third of the 1.3 million people who applied for Employment and Support Allowance were found to be fully capable of working.
Last night Chris Grayling, the Employment minister, said made “real efforts to improve” the WCA and that the government had already implemented several recommendations urged by Prof Harrington.
“Even though no system is ever perfect, his most recent recommendations reconfirmed that the assessment is the right process,” he said.
“The reason why we reassess people who are on sickness benefits is that all the evidence is that a substantial proportion can return to some form of work. We have no financial targets for this.
“We simply believe that people who can work are better off being helped to do so, even if it can be a difficult and stressful process, rather than simply being abandoned on benefits for the rest of their lives. It’s about saving lives, not saving money.”