The incident happened on Monday as the players were travelling back to their hotel after the first day's play in the second and final test against Bangladesh in Chittagong's Zahur Ahmed Chowdhury Stadium.
"En route back to the hotel last night a window on the Australian team bus was broken. No one was injured in the incident," CA security manager Sean Carroll said in a statement.
"Team security personnel are currently in discussion with local authorities while they investigate the cause, which is believed to have come from a small rock or stone," he said.
Carroll said Bangladesh authorities were taking the incident seriously and security had been increased along the route on which the team travels between the ground and its hotel.
Bangladeshi authorities, however, suggested the incident could have been an accident.
Chittagong division police commissioner Mohammad Iqbal Bahar said another vehicle escorting the team bus could have kicked up a loose rock, which hit the bus window.
"We inquired into it yesterday. Construction works are going on along the route and one of the escorting vehicles sent the rock flying into the window of the team bus," Bahar told Reuters.
Australia postponed their 2015 tour of Bangladesh because of security fears in the South Asian nation, and also withdrew from the under-19 World Cup there last year for the same reason.
Bangladesh faces a humanitarian crisis as almost 90,000 Rohingya Muslims flee from violence across the border in Myanmar.
It has also suffered periodic attacks by militants, often against foreigners, liberals and religious minorities. Bangladeshi authorities mostly blame such attacks on local insurgents, although the Islamic State militant group and al Qaeda have claimed responsibility for some of the deadly attacks carried out over the past few years.
Carroll said just before the second day's play began in Chittagong on Tuesday that the test would go ahead.
"We are comfortable with the response from the Bangladesh authorities and the increased security presence we have been provided in light of the incident," he said.
(Reporting by Amlan Chakraborty in New Delhi and Serajul Qadir in DHAKA; Editing by Paul Tait)
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