Prime Minister Scott Morrison has spoken with Premier Daniel Andrews as thousands of Victorians remain stranded in NSW.
More than 2300 applications have been made for exemptions to cross the NSW border after it slammed shut on Friday night, with only 175 processed on Sunday.
The leaders discussed the unfolding border situation and other COVID-19 issues over the phone on Monday night.
The prime minister said the federal government was willing to provide support "to get a better pathway home for Victorians as soon as possible", noting wastewater testing had shown no trace of coronavirus outside of metropolitan Sydney and other known hotspot areas.
"So all of regional, rural NSW remains as rural and regional Victoria does and indeed metropolitan Melbourne substantively," Mr Morrison told 3AW on Tuesday.
"That's an opportunity, I think, for Victoria's government to continue to work through those issues."
Victorian federal MP Darren Chester has criticised the sudden border closure and urged Victorian health authorities to show compassion.
Mr Morrison understands his frustration, but respects the state government's right to dictate public health and border rules.
"It would be great to see these things move in the other direction soon, particularly given the success that's been had in both in NSW and Victoria," the prime minister said.
"What we're seeing in relation to both these outbreaks, when you compare it to what happened earlier in the year, they're getting on top of this.
"The systems are working."
His comments come as it emerged a stranded family with a child with disability and another with special needs are among those seeking an exemption to return from NSW.
Former federal Labor leader Bill Shorten says he will be "hitting the phones" on Tuesday after the mother of an 11-year-old child with disability contacted him in a bid to expedite the family's return from the NSW south coast.
He said the exemption system "doesn't seem to be working the way it should" and implored Victoria's health department to speed up the assessment process, which is taking up to 48 hours.
"Let's just get it done quickly," Mr Shorten told Nine's Today program.
"A whole lot of Victorians on holiday (have been) caught off guard, no chance to sort this out.
"We need now the administrative follow-up to help make sure people are not stranded in some really tough circumstances, like the lady I'm talking about."
Victoria recorded three new locally acquired coronavirus cases on Tuesday for a third straight day, along with another case in hotel quarantine.
The new cases came from 32,544 tests, marginally higher than Monday's figure with wait times reducing significantly as testing capacity ramped up further.
Testing commander Jeroen Weimar is confident the Black Rock coronavirus cluster is on a "very positive trajectory".
As of Monday, 24 cases were directly linked to the outbreak - all connected to the Buffalo Smile Thai restaurant in bayside Melbourne and linked back to a cluster in NSW.
More than 1000 primary and secondary contacts are isolating and a growing number of exposure sites have been identified.
New locations were added on Monday in Albert Park, Bentleigh, Brighton, Emerald, Frankston, Keysborough, Melbourne, Nunawading, Springvale.
The state's number of active cases stands at 38.
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