Border families were left scrambling to meet a midnight deadline to renew permits for children to attend school on Monday.
After a two-week extension to education permits expired on Friday, NSW Health Minister Brad Hazzard has blocked kindergarten to year 10 students and teachers and staff who live or work at a school outside the border bubble from accessing permits to attend school on Monday even though the border region remained virus free and new case numbers were coming down in Melbourne.
Those unable to attend school will be going back to home learning with the ban impacting families on both sides of the border.
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Year 11 and 12 students, teachers and staff will be given an exemption to cross the border and continue regular learning.
Browns Plains farmers Neil and Liz Fisher have three children aged 11, 12 and 13 years who attend Trinity Anglican College caught in the crossfire.
Their 13-year-old daughter is already living with an Albury family.
"When the first lockdown was on we were in the middle of sowing crops and home learning was just untenable," Liz said.
"They ended up catching the bus and doing online learning at school.
"We are not crazy busy at the moment, but we can't be tied to the house.
"We've got to spray crops, spread fertiliser, we are weighing sheep, we're marking lambs."
Trinity principal Justin Beckett said the latest changes disadvantaged country students..
"What we've got is rural kids who are being stranded, and we've got regional kids being road blocked," he said.
"Today in Sydney, in Parramatta and Liverpool, students are freely attending face to face classes.
"Here on the border where there are no active cases, we are preventing students living in small towns such as Gundowring, Talgarno and Kiewa, who are already isolated.
"And all this decision does is isolate them further.
"I would like to see the science behind the decision to have kindergarten to year 10 students not coming to school, when there are no active cases."
Other impacts from the changes will be schools left without principals and the Osbornes Flat Primary School has already moved its entire student population to Baranduda.
Member for Benambra Bill Tilley said the overnight changes were cruel and hypocritical.
"This completely ignores the plight of so many students, teachers and families on both sides of the river," he said..
"It also ignores the fact that COVID cases are falling in Melbourne.
"I don't think NSW Health gets that remote or flexible learning doesn't mean that there are not kids at school, that teachers aren't needed, that the school principal needs to be there.
"And what about some of the schools in the Upper Murray that have students from NSW.
"They have been scarred by the fires, technology cannot overcome the shortcomings of the internet and topography.
"They desperately need social interaction with their school friends."
Mr Tilley also took a swipe at NSW Deputy Premier John Barilaro.
"Why wouldn't I be angry," he said.
"Yesterday the Deputy Premier said that a serious amount of notice and communicating the message was how they would build trust going forward.
"This is then thrown at us in the dead of night, effective from the end of today.
"John Barilaro should be outraged too."