The 45-year-old guided the side to the top of the ICC Test rankings and three Ashes series victories during his time in charge.
However, his role came under scrutiny after England lost 5-0 to Australia in the recent Ashes series Down Under.
In a statement, ECB chairman Giles Clarke said: "Andy Flower has not only shown himself to be a coach of great quality but also a man of great integrity. He has led England to great successes during his reign as team director and I look forward to his continued input in the ECB's coaching structure.
"I am sure that he will be every bit as successful in that role as he has been in his five years as England Team Director. I thank him for his contribution to England's cricketing history and wish him well in the future and his continued role in England's cricketing success."
Flower was appointed England coach in 2009.