India captain Ajinkya Rahane and other senior players spoke to the umpires at the end of the third day's play after quicks Jasprit Bumrah and Mohammed Siraj complained of hearing racist slurs while fielding near the boundary rope.
"Cricket is a gentleman's game and these kinds of things are not allowed or accepted."
There will be a new-look attack with Umesh Yadav out of the series after hurting his calf and T. Natarajan called up as a replacement. India were already without injured regulars Mohammed Shami and Ishant Sharma.
All arrivals enter mandatory hotel quarantine on their arrival, which Australia credits as central in it avoiding high coronavirus numbers compared with other developed nations.
All-rounder Cameron Green is guaranteed to make his test debut if he clears concussion protocols but Paine said Green would not be considered for the opening role.
India A made 194 in their first innings of the pink-ball warm-up match in Sydney, before Shami, Jasprit Bumrah and Navdeep Saini skittled Australia A for 108.
Warner's absence is a major blow for Australia, who lose one of their best batsman and a player who has been a rock at the top of the order for most of a decade.
Unchanged India are chasing a 3-0 series sweep in Australia for the second time in five years after losing the preceding one-day international series 2-1.