With few Border schools unaffected by the COVID-19 outbreak, contact tracers are feeling the pressure.
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St Monica's held a pupil-free day yesterday and will be in remote learning until further notice.
Principal Jacqui Partington wrote in a letter to families there were three cases connected to the school.
"We are doing everything we can to ensure the health and safety of our whole school community," she said.
"The local Public Health Unit has advised that they cannot cope with the current volume associated with school outbreaks.
"We have worked through our contact tracing, and have advised those students to test and isolate."
Both St Monica's and Wangaratta High School have requested parents advise them if their child tested positive.
Albury Wodonga Health chief executive Michael Kalimnios confirmed schools would now lead the management of cases and agreed with Ms Partington's appraisal.
"Given we've now got such a large spread of COVID throughout Victoria, the ability for public health units across Victoria to do the detailed contact tracing ... is very limited," he said.
"Effectively, we don't have secondary close contacts anymore, it's very much for schools and indeed, businesses, if they're identified as having a link with a positive patient to manage that.
"The Department of Education and Training will notify close and casual contacts of confirmed cases and provide appropriate health advice directly, so you won't be contacted by the public health unit - it will come from schools."
Mr Kalimnios acknowledged there was potential not all school cases would be linked, but growing vaccination rates would address risk.
"The Department of Education has been working with Health, just to make sure that as we move into the living with COVID environment, there's a very clear protocol," he said.
"Schools and early learning centre outbreak management plans have been developed.
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"Both in NSW and Victoria, there's a very strong determination not to have unnecessary school closures.
"Single cases and exposures are unlikely to result in extended school closures, however short closures may be required to assess who has been in contact with the case and to undertake notifications.
"Only high-risk contacts will quarantine, for either seven or 14 days depending on vaccination status."