With play resuming on day four in Mackay on Sunday, India's players were told by umpire Shawn Craig the ball had been changed as it had been tampered with.
"When you scratch it, we change the ball. No more discussion, let's play," Craig could be heard saying on the stump microphone.
India's wicketkeeper Ishan Kishan was then put on report by Craig for telling the umpire it was a "stupid decision".
"You will be on report for dissent, that is very inappropriate behaviour," Craig replied.Â
"Because of your actions we changed the ball."
Kishan is not part of India's Test squad for the Border-Gavaskar Trophy, which begins in Perth on November 22.
Fast bowler Prasidh Krishna, allrounder Nitish Kumar and batsman Abhimanyu Easwaran are the only players in the India A side that form part of the Test squad.
There is no indication at this stage of who umpires believe was responsible for the alleged tampering.
Australia were on track to claim victory in the A-match early on day four, with Nathan McSweeney passing the half-century mark in his push for a Test spot.
12°C