She said three unidentified people were seen walking away with team shirts during an evacuation after a basement fire on Friday while the laptop was taken from a room on the fifth floor.
"That is concerning," she told a news conference, adding that the security presence had since been increased with four private guards on the entrance doors and more noticeable identity checks.
"When you have got 15,000 beds, there are a lot of people walking around the village. I'm not accusing anybody but there are a lot of non-accredited workers, cleaners, housekeepers, maintenance workers still walking around.
"Unfortunately in an area of that size with the number of buildings and rooms that there are, theft is going to be inevitable."
Asked about safety implications, at a time of heightened concern about potential terror attacks, Chiller said nobody felt unsafe but all team members had been reminded to keep doors locked and valuables secure.
The theft is the latest in a string of incidents affecting the Australians, their woes perhaps highlighted by the team holding daily briefings where others have not.
Chiller complained last weekend about exposed wiring and blocked toilets, saying the accommodation was "not safe or ready" for athletes who were put up in hotels while contractors rectified matters.
The basement fire was blamed on a cigarette discarded into debris left after the repairs.
The Australians subsequently discovered that the alarm system had been deactivated without them knowing while workmen were fixing the neighbouring building.
Chiller said all debris had now been cleared and a report into the fire received from organisers had recommended the civil and military fire brigades improve communication. There was also a pledge that the smoking ban would be enforced.
Apart from the missing laptop, IT equipment had also been "rifled through".
Chiller could not say whether the laptop contained sensitive data, and neither could she state how many shirts were missing.
"They were our 'Zika' shirts - long-sleeved yellow shirts that had just been delivered to the village and we had them all lined up in piles on the reception desk, in an outdoor common space," she said.
Visitors to Brazil are advised to wear long-sleeved shirts as a precaution against the mosquito-borne Zika virus linked to birth defects in newborn babies and possible neurological problems in adults.
