Some National Broadband Network customers will pay more for their internet or receive a lower-quality service as a result of the "multi-technology" model being used in the rollout, the government's independent infrastructure adviser has warned.

The major Infrastructure Australia audit of the nation's future transport, energy, water and telecommunications needs highlighted poor quality broadband connections, increased costs, and an "inherent tension" between NBN Co's obligations to customers and taxpayers.

Infrastructure Australia has warned the NBN faces major challenges. Credit:Katherine Fenech

The report pointed to a fundamental challenge facing the $51 billion project as it seeks to provide quality, accessible and affordable internet connections for the market while also making a return on taxpayer investment.

The report noted the shift from Labor's original fibre-to-the-premises model to the government's mixed technology model, and said there were increased capital and maintenance expenses for certain connections under the Coalition's rollout.