According to the Daily Telegraph, new managing director of the England and Wales Cricket Board, Paul Downton, told Flower on Thursday that he would be leaving his position.
During his time in charge, the former Zimbabwe wicket-keeper batsman helped England to win the Ashes three times and also masterminded their first World Twenty20 title in 2010.
Flower also helped to steer England to number one in the world test rankings in August 2011 following a 4-0 home victory over India.
(Reporting By Michael Hann, editing by Pritha Sarkar)