An Education Department spokesperson confirmed police attended Wangauni Park Secondary College, McGuire College and Shepparton High School to "conduct safety checks".
“As a precaution, a number of surrounding primary schools were also advised to activate their emergency management plans,” the spokesperson said.
“In every case, once police advised that the schools were safe, they quickly returned to their normal daily routine.”
McGuire College principal John Sciacca confirmed the school received a call about a bomb threat around 9.20am yesterday.
“We followed our evacuation plan to ensure the children's safety and the police came through... the school community was notified of the incident,” he said.
Mr Sciacca said police confirmed there was no threat to the school and all returned to normal about 10.10am.
Shepparton High School principal Christine Cole said students were evacuated from the school onto the oval while police investigated the "potential threat".
Ms Cole said the student safety procedures lasted for almost one hour until police deemed the school site safe.
“Messages were sent to parents and families... everything was safe it was all just a safety precaution,” she said.
Guthrie St Primary School confirmed they also went into lockdown shortly after 10am yesterday after receiving a precautionary message from the Education Department.
Leading teacher Lisa Day said she believed a secondary school in the area received a threat and to ensure safety other schools were told go into lockdown.
Wanganui Park Secondary College and Gowrie St Primary School also confirmed they went into lockdown yesterday morning. The News believes Gowrie St went into lockdown for a second time that afternoon.
An Education Department spokesperson confirmed yesterday's incident was the second of its kind for Wangauni Park Secondary College this week with police attending the school on Wednesday to conduct similar safety checks.
They assured the lockdowns did not disrupt any VCE exams sitting at the time.
A police media spokesperson confirmed an investigation had been launched and remained ongoing.