Australian Chef de Mission Kitty Chiller, who has had to deal with her team's discontent, said a laptop and Zika-protective team shirts had been stolen by people who entered the building during the evacuation.
Approximately 100 athletes were evacuated Friday after a small fire broke out in the basement car park of the Olympic Village apartments housing the Australian team.
"When I arrived midway through the evacuation, I saw three fire (marshals) walking out with our team shirts," Chiller told reporters. "I should take back fire marshals -- I don't know who they were. They were not team members."
Chiller said she did not question the three people as she believed they had been gifted the shirts as a thank you.
"I didn't know if they were volunteers who had been given a shirt because they'd helped us," she continued. "But it doesn't seem to have been what happened."
The shirts were the team's long-sleeved "Zika shirts," designed to protect athletes from the mosquito-borne Zika virus. The shirts had only been delivered on the morning of the fire.
A laptop was also reported missing from one of the cycling officials staying on the fifth floor.
The Australian team were equally annoyed that the fire alarms had been deactivated in their building, which meant veteran shooter Warren Potent actually slept through the entire evacuation.
"I didn't know it even happened, to be honest," Potent told reporters Saturday.
Chiller said the alarms had been disabled without the knowledge of anyone on the Australian team, while maintenance work was being carried out on the building next door.
"Obviously that is completely unacceptable that (a) the fire alarm was disabled and (b) that if it had to be, that we weren't warned about that," she said.
An investigation is now underway involving Rio 2016 and the Australian Olympic Committee.
This is the latest in a number of issues afflicting the Australian team, who only moved into the athlete's village Wednesday, three days after the official opening.
The Rio 2016 organizing committee was not immediately available for comment when contacted by CNN.