The money was loaned to the company by the government to negate the need to approach private companies for funds to build the network, the Australian Financial Review reported.
The ANAO report was also critical of the oversight and risk assessment in loaning the amount, blaming the Department of Communications for not developing processes to manage associated risk.
With the end of the network rollout due next year, there has been speculation as to what the government will do to bring the network up to speed, as the use of copper and HFC has left many users struggling with very poor speeds and unreliable connections.
The ANAO report said: "Communications was not able to provide evidence of their undertaking of the evaluation and assessment in establishing the loan, including suitability of the terms and conditions within the contract.
"[It also didn't provide evidence of] ongoing monitoring of NBN Co’s compliance with several aspects of the loan agreement, and an analysis to progressively assess NBN Co’s capacity to fully repay the loan."
The AFR quoted Communications Minister Paul Fletcher as saying he was confident that the NBN Co and his department were aware of their responsibility in handling the loan.