Five rooms at the Jet Park quarantine hotel have been damaged by recent guests.
In one of the rooms, staff found a hole punched in the door, the curtain rail pulled down, and a hole in a double glazed window.
The guest also damaged a chair, the TV remote, the phone and the alarm clock.
An MIQ spokesperson said four rooms had minor damage like ripped curtains, stained carpets, a broken chair and children's drawings on the walls.
It comes amid hundreds of community cases being quarantined at the hotel.
Joint Head of MIQ Brigadier Rose King said returnees have months to prepare for their time in MIQ but community Covid-19 cases move into quarantine at short notice.
She said understandably, it can be "incredibly stressful" as they rearrange their lives.
"We do acknowledge the additional stress experienced by those in our community who unexpectedly need to enter quarantine facilities," she said.
King did not say whether there had been repercussions for the guests but said any poor behaviour by people in MIQ facilities was taken very seriously.
"We actively encourage staff to speak-up about any concerns they may have, whether they relate to safety or other issues."
She said security at the site is made up by police officers, Defence Force staff and the Aviation Security Service, working alongside private security guards.