Samuel Kasumu was hired as the special adviser to the prime minister on civil society but he will leave his post in May, according to Politico.
The timing of Kasumu’s departure comes after the landmark report by the Commission on Race and Ethnic Disparities faced heavy criticism over its findings, with claims that it is culturally deaf, out of step with public opinion, and “steeped in denial”.
However, Downing Street sources insisted his departure was “absolutely nothing to do with the report”, while a No 10 spokesman said Kasumu had planned to leave the government in May “for several months”.
The spokesman said: “Mr Kasumu has played an incredibly valuable role during his time at No 10.
“As he previously set out, he will be leaving government in May – this has been his plan for several months and has not changed.
“Any suggestion that this decision has been made this week or that this is linked to the CRED report is completely inaccurate.”
Government minister Gillian Keegan appeared unaware of Kasumu’s departure, telling Times Radio on Thursday morning: “I don’t even know who he is.”
She later added that it was a "personal matter".
Shadow women and equalities secretary Marsha de Cordova said Kasumu's departure after the report was published "is telling of how far removed the Tories are from the everyday lived experiences of black, Asian and ethnic minority people.
She added: “Their divisive report appears to glorify slavery and suggests that institutional racism does not exist despite the evidence to the contrary. It is no wonder they are losing the expertise from their team.”
Watch: Race report is 'fantastic, honest, evidence based'
Kasumu will stay in post until next month so he can continue work on improving vaccine uptake in minority groups, Politico added.
The website said Kasumu notified the prime minister’s chief of staff, Dan Rosenfield, of his decision to quit his job – which paid up to £75,000 – last week.
He has reportedly been unhappy in government for some time, with a resignation letter drafted – but then retracted – in February.
In the letter, which was obtained by the BBC, Kasumu accused the Conservative Party of pursuing “a politics steeped in division” and suggested equalities minister Kemi Badenoch may have broken the ministerial code in her public spat with a journalist.
Kasumu wrote that he "fear for what may become of the [Conservative] party in the future by choosing to pursue a politics steeped in division".
The government-backed race review, that was published on Wednesday, said Britain is no longer a country where the “system is deliberately rigged against ethnic minorities”.
Its chairman, Tony Sewell, said it had found no evidence of “institutional racism”, and the report criticised the way the term has been applied, saying it should not be used as a “catch-all” phrase for any micro-aggression.
The commission, that was launched by the prime minister last summer in the wake of the Black Lives Matter movement, said geography, family influence, socioeconomic background, culture and religion all affect life chances more than racism.
Its findings have been described as insulting and divisive, and Sewell has been accused of putting a “positive spin on slavery and empire” when explaining its recommendation on teaching history in schools.
Rehana Azam, national officer of the GMB union, said the report "actually gaslights Black Asian Minority and Ethnic people and communities".
The report proposes a Making Of Modern Britain teaching resource to “tell the multiple, nuanced stories of the contributions made by different groups that have made this country the one it is today”.
Sewell’s foreword to the report, he said the recommendation is the body’s response to “negative calls for ‘decolonising’ the curriculum”.
He wrote that the resource should look at the influence of the UK during its Empire period and how “Britishness influenced the Commonwealth” and how local communities influenced “modern Britain”.
He added: “There is a new story about the Caribbean experience which speaks to the slave period not only being about profit and suffering but how culturally African people transformed themselves into a remodelled African/Britain.”
Highlighting the passage on Twitter, shadow women and equalities secretary Marsha de Cordova said it was “one of the worst bits” of the report which was “putting a positive spin on slavery and empire”.
Halima Begum, chief executive of race equality think tank the Runnymede Trust, said: “Comments about the slave trade being a Caribbean experience, as though it’s some kind of holiday… this is how deafening it is, cultural deafness, it’s completely out of kilter with where British society is, I believe.”
Watch: Commission chair: Institutional racism 'devalued as a term'