The Socceroos' quest to seal automatic World Cup qualification has been handed a potentially seismic blow with star midfielder Jackson Irvine sustaining a foot injury.

Irvine's Bundesliga club St Pauli confirmed the news on Wednesday, claiming the midfielder had experienced pain in the club's 2-1 victory over Holstein Kiel last weekend.

German media said Irvine would certainly miss this weekend's game with Bayer Leverkusen and could be sidelined even longer.

While no timeline has officially been put on when Irvine might return to full fitness, there is obvious concern for Socceroos coach Tony Popovic.

Irvine has been an ever present for Australia under Popovic and his presence at the heart of midfield would be hard to replace at such short notice.

The Socceroos face their biggest games of the qualification window when they play their final two group matches in June.

Australia are due to meet the already-qualified Japanese in Perth before travelling away to face their nearest challengers to second spot in Saudi Arabia.

The Socceroos are a win ahead of the Saudis on the table but can ensure their qualification for next year's tournament in North America with victories across both games.