Johnson, 40, made the comments in 2012 while appearing on a BBC1 series called 'The Big Questions', during which he opted not to back the FA anti-homophobia campaign.
His remarks were brought back into focus after his appointment to the FA body, although Johnson said last week that his views had changed.
The FA announced on Tuesday: "The FA can confirm that Michael Johnson has voluntarily stepped down from his role on the Football Association's inclusion advisory board with immediate effect."
Johnson said in a statement released by the FA: "I've taken time over the weekend to reflect on the media coverage from last week and feel that it's in the best interests of all concerned if I step down from my duties with the inclusion advisory board."
Former Jamaica international Johnson, who played for Notts County, Derby and Birmingham, said he would continue to back anti-discrimination ventures in football.
He said: "My position on the inclusion advisory board was voluntary and I've decided to use that time to continue my personal development and education within equality.
"I remain a big advocate of inclusion in football and have actively supported the FA's COACH programme which offers aspiring coaches from black and minority ethnic backgrounds a chance to progress their football qualifications."
Human rights campaigner Peter Tatchell accused the FA of "double standards" over Johnson's appointment to the 10-person panel when the television footage resurfaced, and questioned whether his past had been thoroughly looked at.
The body set up to advance equality in the game is chaired by FA board member Heather Rabbatts and includes former England international Graeme Le Saux.
Rabbatts said following Johnson's announcement: "It's unfortunate that Michael has decided to step down but he remains 100 per cent behind the aims of the inclusion advisory board and is someone that we will be speaking to on a regular basis as we progress throughout this year and beyond.
"He has a wealth of experience in both domestic and international football and is carving out a coaching career with Birmingham City so he's someone that can bring vital expertise to the work of the inclusion advisory board over time."
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