Officials at Downing Street have been accused of rewriting much of its controversial report into racial and ethnic disparities, despite appointing an independent commission to conduct an honest investigation into inequality in the UK.

The Observer has been told that significant sections of the report published on 31 March, which were criticised and debunked by health professionals, academics, business chiefs and crime experts, were not written by the 12 commissioners who were appointed last July.

The 258-page document was not made available to be read in full or signed off by the group, which included scientist and BBC broadcaster Maggie Aderin-Pocock and Samir Shah, former chair of the Runnymede Trust, nor were they made aware of its 24 final recommendations. Instead, the finished report, it is alleged, was produced by No 10.

Kunle Olulode, an anti-racism activist and director of the charity Voice4Change, is the first commissioner to condemn the government publicly for its lack of transparency. In a statement to the Observer, Olulode’s charity was scathing of the way evidence was cherrypicked, distorted and denied in the final document.

“The report does not give enough to show its understanding of institutional or structural discrimination … evidence in sections, that assertive conclusions are based on, is selective,” it said. “The report gives no clear direction on what expectations of the role of public institutions and political leadership should be in tackling race and ethnic disparities. What is the role of the state in this?”

One commissioner, who spoke out on condition of anonymity, accused the government of “bending” the work of its commission to fit “a more palatable” political narrative and denying the working group the autonomy it was promised.

“We did not read Tony’s [Sewell] foreword,” they claimed. “We did not deny institutional racism or play that down as the final document did. The idea that this report was all our own work is full of holes. You can see that in the inconsistency of the ideas and data it presents and the conclusions it makes. That end product is the work of very different views.”

The commissioner revealed that they had been privy only to the section of the report they were assigned, and that it had soon become apparent the exercise was not being taken sufficiently seriously by No 10.

“Something of this magnitude takes proper time – we were only given five months to do this work, on a voluntary basis,” they said. In contrast to the landmark 1999 Macpherson report, an inquiry into the death of Stephen Lawrence, or the 2017 Lammy Review, both of which took 18 months to conclude, the report by the Commission on Race and Ethnic Disparities (Cred) was not peer reviewed and was published just seven months after the group first met on a videocall.

The group, led by Sewell, was set up by Samuel Kasumu, No 10’s most senior black special adviser, who resigned from his post on the day the report was published, aghast at its final findings. Accusations that Munira Mirza, director of No 10’s policy unit, was heavily involved in steering the direction of the supposedly independent report were not directly addressed by a No 10 spokesperson, who said: “I would reiterate the report is independent and that the government is committed to tackling inequality.”

A source involved in the commission told the Observer that “basic fundamentals in putting a document like this together were ignored. When you’re producing something so historic, you have to avoid unnecessary controversy, you don’t court it like this report did. And the comms was just shocking.”

While the prime minister sought to distance himself from the criticism a day after its publication, unusually it was his office rather than the Cred secretariat which initially released the report to the press.

A spokesperson for the race commission said: “We reject these allegations. They are deliberately seeking to divert attention from the recommendations made in the report.

“The commission’s view is that, if implemented, these 24 recommendations can change for the better the lives of millions across the UK, whatever their ethnic or social background. That is the goal they continue to remain focused on.”