Socceroos coach Graham Arnold has tested positive for COVID-19 for a second time, throwing Australia's preparation for the crunch World Cup qualifier against Japan into chaos.

Arnold tested positive on a routine PCR test on Thursday, a week before the March 24 clash with Japan in Sydney and in advance of his planned arrival into Socceroos camp on Friday.

The 58-year-old had coronavirus in January and was in isolation for the game against Vietnam in Melbourne, with assistant Rene Meulensteen taking the reins for the 4-0 win while Arnold connected to his coaching staff and squad digitally.

Under NSW Health regulations, Arnold -- who is vaccinated, has had a booster shot and is asymptomatic, would be able to leave isolation on Thursday.

However, he would be required to return a negative PCR test result to be able to take his place on the bench for the crunch qualifier against Japan.

"Football Australia today advised that Socceroos head coach Graham Arnold has unfortunately returned a positive COVID-19 result prior to travelling to Socceroos camp in Sydney," the FA said in a statement.

"Arnold returned the positive result after following national team protocols, which saw him conduct a PCR test on Thursday ahead of his planned arrival into camp today.

"Arnold will now follow NSW Health guidelines and self-isolate at home.

"Until his period of self-isolation concludes, Arnold will remain connected to Australia's squad and staff digitally, as he successfully did in January when Australia played Vietnam in Victoria."

Arnold had a press conference in person on Thursday, with the FA contacting media who attended regarding the positive test.

Next week's clash with Japan in Sydney and the March 30 away game against Saudi Arabia are must-wins if the Socceroos are to secure automatic qualification for Qatar 2022.

Australia are third in their group on 15 points, four adrift of leaders Saudi Arabia and three behind Japan, which would force them into the unwanted play-off route.

Aaron Mooy (COVID-19) and injured pair Adam Taggart and Riley McGree are among the absentees in an understrength squad for the two games, which was headlined by Bruno Fornaroli's shock inclusion.