The incident happened around 8.20am as children were on their way to school.
Two fire engines were in attendance and were still there as the Herald went to press later the same day.
Scottish Fire and Rescue said they had responded to an alarm call at the school and added there were no reports of any injuries.
Several teachers who were inside the building at the time were evacuated and pupils found themselves locked out for up to two hours.
Lenzie Academy informed parents on its official Twitter account that there “had been an incident” at the school, posting that the fire service was in attendance and the building had been evacuated.
A tweet later in the morning stated: “The fire service have advised that pupils and staff can return to classes. There is a small section of the school that has been isolated and will not be used for the remainder of the day.”
East Dunbartonshire Council boss Ann Davie said on Monday: “On arrival this morning, a member of janitorial staff noticed a smell coming from an isolated part of the school. The smell was not of natural gas and no alarms were activated.
"As a precaution, pupils and staff were not allowed into the building untilthe situation was assessed by the fire service.
"Pupils and staff are now back in the school. The affected area has been isolated and is being investigated.”
In an update last night, Ms Davie added: "Following investigations earlier today, the source of the smell was identified as coming from an old fridge in the staff area which had developed a leak over the weekend. The appliance has now been removed."