Victoria's three A-League teams remain stranded in Melbourne after plans to fly players and staff to Canberra fell through for the second time in as many days on Tuesday night.

Melbourne Victory, Melbourne City and Western United players and staff met at AAMI Park on Tuesday evening and took buses to the airport for a flight to Canberra.

The three clubs then planned to travel on to NSW from Canberra when possible.

But while on buses waiting to enter the airport hangar, they received advice they would have to quarantine for 14 days in Canberra and not be able to train in that time.

The clubs made a collective decision not to travel Tuesday night and will instead stay in Melbourne for the immediate future while they await the NSW government's call on exemptions.

United are scheduled to play Victory on July 16, then City four days later.

FFA had sought an exemption from the NSW government for players and staff to travel interstate after the clubs did not leave Victoria before the midnight Monday deadline for Melbourne residents.

On Tuesday, NSW deputy premier John Barilaro indicated the government would work with FFA to help the Victorian clubs cross the border and into their NSW hub.

"You've heard me on the NRL and the importance of sport and I think we've got to work with the FFA, so I'll be reaching out to the FFA today and then see what they need," Barilaro said.

"But yeah of course, if we've got an opportunity to do so, let's bring them across the border, let's park them in the regions or here in the city and make sure they're part of the A-League that kicks off shortly.

"We'll work through it. I think there is a real opportunity to do it. The exemptions exist and we'll work with health officials as we've done previously with all the other codes."

Western United chief executive Chris Pehlivanis was optimistic of securing an exemption.

"The discussions have already started," Pehlivanis told AAP on Tuesday afternoon.

"Now in terms of timing, we're not sure - it could be quick, it could be a couple of days - but we're planning to be there (in NSW), subject to government."

The three clubs had originally planned to fly out on a charter plane on Tuesday morning - before the full Victoria-NSW border closure at midnight.

However, the league appeared to have been caught on the hop by the decision to close the border to Melbourne residents a day earlier.

Victory, City and United scrambled on Monday night, getting players and staff to the airport in a bid to fly to Canberra.

The players and staff boarded the plane, only for the flight to be cancelled due to poor visibility at Canberra Airport, leaving them stranded on the tarmac.

The 10 AFL teams, the NRL and Super Rugby had made earlier moves to get their teams out of Victoria amid the state's coronavirus spike.

Last last night, the FFA released a statement defending the debacle.

"After the NSW Government’s decision to close its border with Victoria, active discussions occurred throughout the day to seek to obtain an exemption under the NSW Public Health (COVID-19 Interstate Hotspots) Orders for the teams to enter NSW," said the FFA.

"In addition to seeking an exemption to enter NSW directly, on an alternative plan was developed to move the players and high-performance coaching staff to Canberra this evening, however, within the tight timeframes available ACT Government quarantine regulations could not be met."

"We did absolutely everything we could to get the players and staff out of Victoria by midnight, but in such a rapidly evolving situation, unfortunately it was just not possible," said Head of Leagues Greg O’Rourke.

“We are in discussions the NSW Government, and we will continue to seek the exemptions necessary for the teams to travel.

“Given the strict League and Club Protocols our Teams have been following since 2 June 2020, combined with the fact we have not had any Players or High Performance Staff return a positive COVID-19 testing result, we feel that we have a very good case to gain the exemptions and get the teams to NSW to complete the Hyundai A-League season, and we will make every attempt to do so.”

O’Rourke added: “I’d like to sincerely thank the players, their families and staff from the three clubs for their understanding and commitment this past 24 hours. T

"he disappointment of getting prepared to travel out of Victoria to prepare for the restart not once but twice has been most frustrating for them and can assure them, the clubs’ members and fans that we are all committed to overcoming this evolving challenge and to play football again.”