Hardik Pandya was back in Mumbai after being released by the National Cricket Academy (NCA) this week, having failed to recover from his left ankle injury.
A sudden flare-up ruled him out of the World Cup though the all-rounder had started to bat at nets recently, sources told The Telegraph.
The medical team at the NCA after consultation with specialists were of the opinion that he needed more time to regain fitness.
The development was kept under wraps by the BCCI and the team management until the event technical committee made the announcement on Saturday morning. Captain Rohit Sharma had said in Mumbai on Wednesday that Pandya was being assessed on a daily basis.
Pandya had suffered ligament damage while trying to stop a ball on his follow-through against Bangladesh in Pune.
Prasidh Krishna, who has played 17 ODIs, was approved as his replacement. The right-arm pacer has picked 29 ODI wickets at an average of 25.58.
"Tough to digest the fact that I will miss out on the remaining part of the World Cup. I'll be with the team, in spirit, cheering them on every ball of every game... This team is special and I'm sure we'll make everyone proud," Pandya wrote on X.
Head coach Rahul Dravid admitted that Pandya was the one player the team didn't have a backup for.
Prasidh made his return in August from a long layoff owing to a stress fracture of the back.
India will have to go in with only five specialist bowlers hoping none has an off day.