Delivering the order, the single bench of Justice R R Prasad said there was no evidence to find Chakraborty guilty.
Chakraborty had moved the high court after the lower court had sentenced him to four years prison term and slapped a fine of Rs 3.5 lakh in a case pertaining to alleged fraudulent withdrawal of Rs 39 crore when he was the deputy commissioner of Chaibasa between 1993 and 1996.
He was heading the State Institute of Rural Development when a special CBI court held him guilty on July 26, 2008, which led to his suspension.
Previously, the officer had been discharged in two other cases in the lower court.
A CBI official said the agency would move to Supreme Court against the verdict.