Players and staff were travelling from Busapara Stadium back to their team hotel in the eastern city when the rock pierced the window on the right-hand side of the bus, CA said on its website.
The board said the rock was "believed to be roughly the size of a cricket ball" and had ended up inside the bus.
"In a remarkable piece of good fortune, no one was sitting on the seat next to the window when it was broken," CA's report said.
"While no one was injured, the Australian players were understandably shaken up by the incident."
Australia's team bus was also struck by a rock in Bangladesh five weeks ago as it travelled back to a hotel following the first day's play of the second and final test against the home side in Chittagong.
That prompted authorities to tighten security around the Australia team.
Australia opening batsman Aaron Finch posted a photo of a shattered window on a bus on Twitter.
"Pretty scary having a rock thrown through the team bus window on the way back to the hotel!!" he tweeted.
Pretty scary having a rock thrown through the team bus window on the way back to the hotel!! pic.twitter.com/LBBrksaDXI— Aaron Finch (@AaronFinch5) October 10, 2017
Assam Chief Minister Sarbananda Sonowal condemned the attack and said that anti-social elements were behind the attack and that the culprits would be put behind bars soon. MLA Himanta Biswa Sarma also apologised to the Australian team and promised to punish the guilty.
Our deep apology. People of assam never endorse such behaviour.we will punish the guilty. https://t.co/3IYYSoME0y— Himanta Biswa Sarma (@himantabiswa) October 10, 2017
The Australian team are scheduled to play India in the third and final Twenty20 of the series in Hyderabad on Friday.
(With Reuters inputs)
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First Published: October 11, 2017, 8:36 AM IST