The BBC has removed him as a presenter on tonight’s Tuffers and Vaughan Show on 5 Live after it was claimed he made a racist comment to a group of Asian players.
Mr Vaughan was named in Yorkshire County Cricket Club's report into Azeem Rafiq's claims of racism during his time at the club.
“The BBC takes any allegations of racism extremely seriously,” a BBC spokesperson said.
“We have made the editorial decision that Michael won't appear as a presenter on 5 Live's Tuffers and Vaughan Show on Monday.
“The show focuses on topical discussion around current cricketing matters and given his personal involvement, we need to ensure we maintain the impartiality of the programme.”
They said the BBC remains in discussions with Michael and his team.
Mr Vaughan has said he “totally denies any allegation of racism”.
He categorically denied suggestions he told a group of non-white team-mates there were “too many of your lot, we need to do something about it” over a decade ago.
The 2005 Ashes-winning England captain has been silent on his Twitter account since the row broke last week, with no posts since Thursday, when he tweeted an article he had written for the Daily Telegraph denying the allegations.
Lord Kamlesh Patel has been appointed Yorkshire chairman after previous chairman Roger Hutton resigned over the county's handling of the Azeem Rafiq case.