Alfred Deakin High School is the third Canberra school to be dealing with lead paint contamination since the July school holidays.
An ACT Education Directorate spokesman said the lead dust was discovered in August during construction work on the school hall.
A licenced assessor found four samples taken from the ceiling and floor cavities returned a reading above the acceptable threshold of 0.11 milligrams per square metre (mg/sq m).
The readings ranged from 1.33 mg/sq m to 3.22 mg/sq m.
"This lead dust was only found in non-accessible areas," the spokesman said.
"The removal of this lead dust is now being undertaken as part of the process to replace the roof of the hall."
The spokesman said the discovery of lead dust did not extend the time planned for the roof replacement, which is ongoing.
When Education Minister Yvette Berry was asked if she was concerned that another school was dealing with lead contamination, her spokeswoman said the lead dust at Alfred Deakin High School was only found in non-accessible areas and had been cleaned in line with expert advice.
"Many buildings, including schools, built before 1970 have lead paint. Schools that have lead paint or other hazardous materials have management plans in place, developed with expert advice.
"If parents have concerns they should contact the school or the Education Directorate."
Opposition spokeswoman for education Elizabeth Lee said the presence of hazardous materials should not be a surprise to the government.
"We all know that a lot of Canberra schools were built over 30 years ago and if as the Minister claims there is a maintenance plan in place she needs to revisit that because it's clearly not working."
Meanwhile, five rooms at North Ainslie Primary School were cleaned over the weekend after lead levels up to 117 times the acceptable threshold were discovered.
The rooms - a breakout teaching room, a store room, toilet, staff room and an art store room - will be closed until testing by a licensed assessor confirms they are safe to occupy.
The spokesman confirmed some items were taken off-site for cleaning and a small number of replaceable, low-cost items were destroyed as part of the cleaning process.
"Further testing will be conducted across the school to determine if the issue is more widespread."
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At the beginning of Term 3, 11 classrooms at Yarralumla Primary School were closed for specialist cleaning after lead-painted windows were replaced in the July school holidays.
Students in year 3/4, preschool and the Montessori preschool were moved to other parts of the school for up to six weeks while the cleaning work was being conducted.
Teaching materials worth thousands of dollars were destroyed as part of the clean up. It is unknown how much the Directorate spent on cleaning.
The spokesman said classroom spaces were reopened at Yarralumla Primary School on Monday, August 31 but some non-teaching areas of the school remain closed.
The Education Directorate spokesman said the directorate routinely monitors hazardous materials in ACT public schools that have a hazardous materials plan in place.
"In recent weeks, the Education Directorate has updated policies for building management and communicated this with the schools. Following this, there may be more information of any recent works shared with the Directorate."