Uncapped Queensland seamer Michael Neser takes Hazlewood's place in the touring squad.
"Josh has been managing some low-level bone stress in his lumbar spine for a short period," Cricket Australia physiotherapist David Beakley said on Monday.
"He had a repeat scan and although it has not progressed to a fracture he is starting to experience some lower back pain.
"As such, we are taking a conservative approach and he will not travel to England for the one-day series."
Australia will play five one-dayers and a Twenty20 match against England from June 13-27.
(Reporting by Hardik Vyas in Bengaluru; Editing by Christian Radnedge)
