Kishan sustained a right adductor strain, according to a BCCI statement, during the series opener in Christchurch on Thursday, which the tourists won by four wickets to go 1-0 ahead.
"Ishan Kishan has a niggle in his groin," India batting coach Sitanshu Kotak said at a press conference. "I know there was speculation (about the change in the batting order" but it wasn't a change as such.
"It was because of the groin strain (to Kishan). I think he is unlikely for one game."
Sooryavanshi is now likely to be included in India's line-up after missing the last four T20Is after playing in the semi-final and final of their victorious Asian Games.
The 15-year-old is the most like-for-like replacement for Kishan in the touring squad, with only other option being seam-bowling allrounder Shivam Dube.
Kotak added: "If Ishan can't play - unless he recovers completely, the medical team will tell (us) - then obviously Vaibhav comes into the calculations as a batter. (He is) definitely one of the strongest persons who can play."
India earned their highest-ever T20I run chase when they successfully chalked off New Zealand's 225/4 with four wickets remaining in a run-soaked encounter in Christchurch on Thursday night.
Less than eight overs were bowled in the fifth and final T20I between India and West Indies as heavy rain fell in Bengaluru.
India star seamer Jasprit Bumrah is doubtful to feature during the upcoming five-match ODI series against New Zealand in November despite being fully fit.
Shai Hope hit yet another century while Keema Paul bagged a five-wicket haul as West Indies beat India by 24 runs in the fourth T20I in Hyderabad to level the five-match series at 2-2.
