New Zealand skipper Kane Williamson has been ruled out of the first two ODIs against India as he continues to battle an inflamed AC joint in his left-shoulder and has been replaced by Mark Chapman.

The injury occurred while fielding in the third T20 International in Hamilton last Wednesday and prevented him from playing the final two matches of the series.

Team physio Vijay Vallabh has said they would continue to cautiously manage Williamson's return to play.

"Kane has had an X-ray scan which cleared him of anything serious, but it's best for his recovery that he avoids aggravating the joint for the next few days," Vallabh was quoted as saying by New Zealand Cricket.

"He will continue his fitness training sessions throughout the week and will start batting again on Friday with the prospect of being available for game three next Tuesday."

Selector Gavin Larsen confirmed in-form Auckland Aces left-hander Mark Chapman would join the squad in Hamilton on Tuesday.

"It's hugely disappointing for Kane, but with so much important cricket still ahead this summer we must take a safety first approach," Larsen said.

"It's great to welcome Mark back into the one-day unit off the back of consecutive centuries for New Zealand A against a strong India A side.

"Mark's a versatile player who can cover multiple batting positions and his fielding is a real upshot to have in the squad."

With Williamson ruled out, Tom Latham will captain the side after last leading the ODI team against Bangladesh in Dunedin a year ago.