A media release issued by CA said Hayden was charged under Rule 9 of CA's Code of Behaviour, which prohibits detrimental public comment. CA will appoint a Code of Conduct Commissioner from its panel and convene a hearing at 8 p.m. local time on Wednesday.
Earlier CA had assured the Indian cricket board that it would investigate Hayden's remarks.
"Sutherland (the Cricket Australia chief executive) wrote to me that he is aware of the comment and is dealing with it," Niranjan Shah, the BCCI secretary told reporters.
Shah has asked the Indian team manager Vimal Soni not to react to Hayden's comments.
Harbahjan was quoted by a news agency as saying he did not want a slanging match over the issue.
"Maybe they (Australians) realise they no longer are the undisputed champions of the world. Maybe they feel the crown is slipping. Otherwise, why would a cricket veteran (Hayden) ask a 19-year-old (Ishant Sharma) to join him in a ring? You only need to speak to international cricketers and international teams to know in what opinion they hold Hayden," Harbhajan said.
Hayden and Harbhajan clashed during Sunday's CB Series game between the two sides and the Indian team later complained that Hayden had called Harbhajan a 'mad boy'.
Clarifying, Hayden told the radio station: 'I called him a bad boy'.
He also said: "It's been a bit of a long battle with Harbhajan, the first time I ever met him he was the same little obnoxious weed that he is now. His record speaks for itself in cricket."