The Indian captain blamed the state of the Gabba's practice wickets for injuries to players that had unsettled the team before their batting collapse against Australia on the fourth day.
India officials were fuming after batsmen Shikhar Dhawan and Virat Kohli were struck batting in the outside nets before day four's play.
Dhawan took a blow on his right wrist and retired hurt on his overnight score of 26 before resuming his innings later in the day and finished as topscorer with 81.
Kohli, nursing a sore forearm, was forced at the last minute to replace Dhawan and walk out with limited preparation to bat at the start of the day with Cheteshwar Pujara.
Dhoni said the incident created ‘unrest’ in the India team dressing room before his side capitulated, at one stage losing 4-11, setting up Australia's four-wicket win that sealed a 2-0 series lead ahead of the third Test which gets underway on Boxing Day in Melbourne.
"He [Dhawan] was a bit uncomfortable, but by the time we came back [from practice] to the dressing room, it was quite close to the start of play," said Dhoni.
"We could only give a five to 10-minute notice to Kohli to go on which was not fair to the batsman.”
Blaming the wicket’s condition after the match, the captain said that the pitch certainly could improve.
"The wicket was not good for practice, I found it to be a bit uneven," he added. “It can certainly improve and I won’t say more as I don't want to create a controversy".
But the practice wickets were not a problem for the Australians as skipper Steve Smith was satisfied.
"No, they were fine," said Smith. "They mirror the exact state of the Test pitch in the middle."
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iam not that disappointed yet, except for rohit sharma ...every one had their moments of glory,but we are two down...unless we win the next game there is no point in all the positives we had so far
When Australia comes to India, they lose 4-0. When India goes to Australia, we lose 4-0. I wonder which is the better team?