The charges stem from the "tentative findings" made last month by the Social Justice and Nation Building Ombudsman, who is looking into alleged discrimination within the sport's national governing organisation in the past.
"While Mr Boucher is being charged with gross misconduct, which could lead to his dismissal, CSA emphasises it is important that the independent inquiry first needs to test all allegations before any question of sanction can arise," CSA said in a statement on Thursday.
Former spinner Paul Adams said he had been called a "brown s**t" in a South Africa team song during his time in the side, which spanned a nine-year period from 1995 to 2004, including by former wicketkeeper Boucher, who has since apologised.
"I look forward to dealing with and defending these allegations which have been made and will do so at the hearing in due course," Boucher said later in a statement.
"For now I am solely focused on my duties as head coach of the Proteas."
The ombudsman's report, submitted to CSA last month, also criticised current CSA director of cricket Graeme Smith and former national team captain AB de Villiers.
The report said their selection decisions made during their times as captain of the side were prejudicial towards Black players.
Smith and de Villiers have denied the allegation.
Boucher is currently in charge of the South Africa one-day international side that is one game into a three-match series at home to India.
His legal team will meet with the chairperson of the disciplinary hearing, Terry Motau, on Wednesday to determine a timetable for the proceedings.
South Africa are due to tour New Zealand for two Tests, with the first starting on February 17.
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