National coach Frank Farina said Australia soccer's worst fears had come true and blamed the sport's national ruling body Soccer Australia (SA).

In a story in the Herald Sun headlined 'Rock bottom', Farina said: 'Our worst fears have come true today.'

'You can't be serious when you are told 12 days before a tournament starts that you are actually going,' he added.

SA has missed out on a potential US $2million including $1million appearance fee after failing to qualify for next year's FIFA Confederations Cup, The Australian newspaper said.

Sunday's loss added to earlier SA dramas including financial and administrative problems and a failure to overcome Uruguay to reach this year's World Cup finals.

'Australian soccer is left to pick up the shattered pieces of a result that could set the game back years,' The Australian said.

'Make no mistake, the defeat by Australia's arch-rivals is almost as close to a disaster as the game has seen.

'This was supposed to be the first, significant step on the road to salvation on and off the field.'

A pay dispute with the players and a court battle with a marketing partner had placed Australia's participation in the Auckland tournament in doubt last month.

'We can't allow it to go on,' Farina was quoted in The Australian as saying.

'If we can't sort something out then we (the game as a whole) may as well throw our hands in the air and walk away.'

Acting SA chief executive Greg Bates said Farina had been handed 'mission impossible' to win in New Zealand.

'If the administration is in disarray, you cannot win on the field,' Bates was quoted as saying in the Herald Sun newspaper.

'People have to accept responsibility about how we got to this position,' he said.