The BCCI, however, did not name any replacement for the fast bowler.
Khaleel, who has played 11 ODIs and 14 T20 Internationals for India, returned with figures of 2 for 46 from his 8 overs in the second one-day match in New Zealand. In the series opener, he had taken four wickets for 43 runs in 9.1 overs.
India A are on a tour of New Zealand for a three-match unofficial ODIs series and two four-day games.
The unofficial ODI series is currently locked at 1-1 after India won the first match by five wickets before losing the next one by 29 runs.
The series decider will be played here on Sunday.