Deakin was made redundant by Port Vale last year when the club went into administration and his appointment has caused anger among some Bury supporters.
The Shakers have had well-documented financial problems, but their future was secured when a takeover was completed in May, with Stewart Day taking over as chairman.
"The club want to make it clear to all concerned fans that Mr Deakin has been employed on a consultant only basis to assist in the reviewing of current contracts and the procedures of the current commercial department," said a Bury statement.
"It was his knowledge and experience that was needed as an immediate input into the turning around of the situation we found ourselves in.
"Mr Deakin is not a shareholder or director and as such reports to the board with all his findings.
"The chairman has full control and would not allow anyone to destroy the amazing work we have done to date and detract from the positive feedback we have had from the loyal fans."