Medium-pacer Hamish Bennett has been called up as his replacement in the Black Caps' squad, which won the first ODI of the five-match series in Napier on Sunday.
The 21-year-old Milne played in the first ODI at Napier on Sunday and picked up one wicket in 7.3 overs that he bowled, before walking off in the 41st over of the Indian chase.
It was only his seventh ODI in a short career so far, wherein he has earned quite a reputation as a tear-away fast bowler.
Milne had an MRI in Hamilton yesterday, after the team arrived from Napier.
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The team's physiotherapist Paul Close said, "The scan showed Milne has torn an abdominal muscle and will need a rehabilitation period of around six weeks."
The young player will also be seeing a specialist in Auckland later today for further assessment.
His replacement from Canterbury, 26-year-old Bennett joined the team in Hamilton ahead of training for the second ODI tomorrow.