A government review into coronavirus risk factors was not led by the health official said to be in charge.
Public Health England announced the inquiry, which investigated the impact of the virus on different ethnic groups, would be led by black doctor Prof Kevin Fenton.
But the BBC understands the report was led and written by Prof John Newton, head of the UK's testing programme.
PHE said Prof Fenton "contributed" to the review.
It added that he led on community engagement, although this work was not included in the final report published earlier this week.
The public health body did not confirm whether responses from at least 1,000 organisations and individuals contributing to the review would be published amid concerns sections of the draft report had been removed.
The rapid review, launched in May, confirmed that people from black, Asian and minority ethnic backgrounds were dying at disproportionately higher rates than white Britons.
PHE's original announcement said Prof Fenton would "lead the review, supported by a wide group including [former UK equality watchdog chief] Trevor Phillips".
And speaking on Thursday, equalities minister Kemi Badenoch said Prof Fenton's involvement was an example of "diversity in leadership".
"It's one of the reasons why we asked Professor Kevin Fenton, who is a black surgeon, to lead on this review," she told MPs.
Patrick Vernon, a social justice campaigner who has recently lost a family member to coronavirus, said the black community felt "misled" by Prof Fenton's involvement and that "trust had been lost".
"The government has said 'black lives matter' but valuable time has been wasted," he said.
"We've lost confidence in the process and want an independent public inquiry."
In May, Prof Fenton told the Royal Society of Medicine at an event attended by the BBC that he had consulted at least 1,000 individuals as part of the government's review.
"The issues of racism, trust, discrimination and stigma are certainly coming up loud and clear from so many of our [community] stakeholders and partners," Prof Fenton said.
Writing on Twitter after the report's publication on Tuesday, Prof Fenton thanked "fellow PHE scientists" who had "led this phase of the work".
He added engagement with "individuals, communities, professionals and leaders" would play "an invaluable part in this next phase".
PHE originally said its findings would "inform actions to mitigate the risks it presents" - but did not explicitly describe the review itself as a two-stage process.
In a statement, PHE said Prof Fenton "contributed" to the review "alongside a wide variety of PHE colleagues".
"Professor Fenton has been engaging with a significant number of individuals and organisations within the BAME community over the past couple of months, to hear their views, concerns and ideas about the impact of the virus on their communities.
"The valuable insight he has gathered will inform the important work the Equalities Minister Kemi Badenoch is now taking forward."
Both the government and Prof Fenton were approached for comment.
Follow Rianna on Twitter @The_Crox