Johnson has troubled the Indian batsmen with his pace in the ODI series which currently stands at 2-2 with the final match in Bangalore on November 2. He is the joint leading wicket-taker in the series with seven from five matches.
CA said they were sending Johnson back to Australia to help him prepare for the Ashes series at home against England.
CA's General Manager of Team Performance Pat Howard said Johnson will return to Australia to prepare for longer form cricket as he stakes his claim for selection in the Ashes series.
"Mitch has performed very well in India, however, we believe it is best for his preparation ahead of a busy summer to have him return home to increase his bowling loads in preparation for the Ashes Test window," Howard said.
Johnson will depart India today for Perth arriving home on Friday, CA said.