An NDIS provider supporting babies and children has been restricted in caring for clients because of the border permit isolation clause.
Noah's Ark has an office in Albury, with five therapists living in the city and three living in Wodonga.
Twenty per cent of their client base, or 21 children, are outside of the blue zone.
Four live in NSW, within 60 kilometres of the border, and 17 are on the Victorian side, living between 25 kilometres and 80 kilometres away.
Staff who visit clients in Indigo, Alpine and Towong are being rendered unable to return to NSW clients for 14 days.
Team leader and occupational therapist Jane Tinkler said it resulted in "significantly reduced access" to specialist therapy and support for some children who were outside the blue zone.
"These children and families have had delays in critical developmental support since March, and this is creating further risk in long term outcomes for these children and families," she said.
Unpredictable wait times at the border crossing have caused unplanned cancellations and loss in staff productivity.
Varying numbers of permit checkers at the checkpoints have been observed and wait times increase significantly when there are less people checking permits.
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Noah's Ark has contacted Indi MP Helen Haines and NSW Cross Border Commissioner James McTavish.