A review of the August 2013 incident found the potential for a serious injury or death to the youngsters was heightened because of electrical cabling in the roof, but the power supply was never switched off.
For this reason police, paramedics, firefighters and Power and Water workers refused to enter the ceiling cavity.
Middlebrook said the increasing number of female detainees posed a serious issue and referred to an alleged sex romp by Don Dale inmates in February 2008.
A media report said boys had allegedly sneaked into the girl's room after dark while other detainees distracted guards for a "Valentine's Day orgy".
Middlebrook said the allegation could not be substantiated, but inadequate infrastructure meant "the potential was there".
The 38-year corrections veteran said before 2007 he'd had no experience in youth justice.
During his tenure as commissioner, he witnessed a spike in destructive behaviour and assaults on staff in youth jails.
There were a number of violent riots and escape attempts, largely due to an increase in the use of drugs such as ice, Middlebrook said.
He also struggled with the daily "crisis" of a rising prisoner population, a poorly trained workforce and severe financial pressures that brought the corrections department to its knees, the inquiry heard.
Middlebrook authorised the tear gassing of six boys in 2014, the scandal that sparked the royal commission.
Middlebrook was forced to resign in 2015 after a rapist and murderer escaped a low-security adult prison work camp.
The incumbent corrections consultant told the commission a "just lock-them-up model" and punitive political agenda has no chance of rehabilitating kids in jail or reducing re-offending.
"Tough on crime means more numbers, more overcrowding and stress on the system ... building prisons is not the answer," he said.
Middlebrook said he was embarrassed to be in charge of a system with one of the world's highest incarceration rates, but he couldn't control successive government policy.
Former corrections minister John Elferink and former Northern Territory chief minister Adam Giles will also give evidence this week.
Prime Minister Malcolm Turnbull ordered the royal commission last year following an ABC Four Corners documentary.