The result leaves the five-time FIFA U-17 World Cup champions without a win after two matches, following their opening 3-2 loss to Tanzania.
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Coach Uwejamomere Eboboritse’s team have now conceded seven goals and scored four, exposing defensive weaknesses the coaching staff will look to improve.
Despite creating attacking opportunities, Nigeria struggled to contain a clinical Australian side that punished mistakes.
The Golden Eaglets will conclude their campaign against hosts China on Saturday as they continue preparations for the WAFU B U-17 Championship in September.
The tournament is part of their build-up for the Africa U-17 Cup of Nations qualifiers.