Socceroos coach Graham Arnold will sit out Wednesday's crucial World Cup qualifier against Vietnam in Melbourne after testing positive for COVID-19.

The 58-year-old is isolating at the team's hotel in a blow to Australia's preparations for the clash at AAMI Park as his squad begins to assemble in Victoria.

Football Australia said in a statement on Sunday that Arnold is fully vaccinated, asymptomatic and received a booster shot 10 days ago.

With Arnold unable to be on the touchline for the clash with the last-placed Vietnamese, he'll be replaced by assistant Rene Meulensteen for the game.

Meulensteen, a former assistant to Sir Alex Ferguson at Manchester United who has been Arnold's number two since mid-2018, will work alongside former Socceroo Tony Vidmar until Arnold is cleared to return to the team.

"My staff and I have always planned that there could be a day that I might not be able to come to a match, so I believe with great planning and people in place, everything will run smoothly this week," Arnold said.

The match, as well as the subsequent game against Oman in Muscat on February 1, are basically must-win for the Socceroos after they failed to win in their past three qualifiers.

Draws against Saudi Arabia and China and a defeat to rivals Japan have left Arnold's team third in Group B of the third stage of Asian qualifying.

Only the top two teams in each group advance directly to Qatar 2022, with the third-placed teams to play each other in a playoff.

The winner of that match-up then takes on South America's fifth-placed team in an intercontinental playoff for a spot at the World Cup finals.

The news comes just days after Arnold admitted he was crossing his fingers that there wouldn't be any COVID-19 dramas as his squad travelled from all over the globe to Melbourne.

Arnold will be allowed to leave isolation on Thursday but his return to in-person national team duties will be subject to clearing additional medical protocols.

AAP