KOONDROOK Primary School students were turned around at the gate on Friday, after emergency services issued an evacuation warning amid concerns about the integrity of the ring levee.
The school is located on a horseshoe-shaped bend on the bank of the Murray River.
"An evacuation warning remains in place as the height of the Murray River has reached the site’s maximum design levee height and concerns remain about the integrity of the levee being maintained with sustained flow," VicEmergency said.
In a statement, the Department of Education confirmed the evacuation order.
"VicEmergency has issued a 24-hour evacuation order today for Koondrook Primary School as a precaution due to water levels reaching the maximum design levee height," the statement read.
"Students are currently being collected by parents and will remain home today.
"A council run kindergarten service, which operates on the school site, was also asked to evacuate."
About 100 children attend the school.
It comes as the Bureau of Meteorology issued a forecast river height of 6.3 metres for Barham early this week.
The river at the border town has been at major flood levels for the past fortnight.
As a precaution, the Australian Defence Force was requested by the incident control centre at Swan Hill to add another bag to the height of the existing sandbag levee at the school and low-lying areas in the township.
"Victoria Police is in town door knocking some places that may be at risk if the levee breaks or persons known that may be generally venerable should an evacuation need to occur and to prompt those people to have things like a plan of what to take, medications, who to notify," the Koondrook CFA posted on social media.
"Currently there are no known breaks or breeches in our levee, and the Koondrook Development Committee and their crew of levee monitors are doing a fantastic job."
The school and local brigade was quick to reassure parents and the community the evacuation warning for the school grounds was a precaution.
"There is no failure of the levee at the school as insinuated and the town is not under any increased threat than what it was when it peaked a couple of weeks ago," it was posted.
Meanwhile, a torrent of water is being released from the Hume Dam following significant rainfall.
Releases from 12 gates at the dam, near Albury, had increased to 75GL per day, up from 50GL per day, in response to inflows that peaked at 100GL a day.
Murray–Darling Basin Authority (MDBA) executive director of river management Andrew Reynold said combined with inflows from the Kiewa River – downstream of Hume Dam – the Murray River was expected to approach or possibly exceed the major flood level at Albury in coming days.
Hume Dam is 96 per cent full, with 124GL of airspace.
The school was contacted for comment.