The £4.2billion super sewer going under the river Thames is being investigated by the National Audit Office.
The Government spending watchdog revealed it was examining the complex funding model as well as the risks faced by taxpayers and consumers.
Taxpayers would be losing out in the event of cost overruns or a financial collapse for the Thames Tideway Tunnel.
The consumer would also have to pay for a third of construction costs through higher water bills.
The audit report, which will also investigate why the tunnel was chosen over greener alternatives, is due to be published in the autumn.
The scheme run by Tideway, the Government company set up to deliver the sewer, is the second biggest project in the capital after Crossrail.
It is the largest investment in London’s sewers since Sir Joseph Bazalgette built the network in 1858.
Tideway chief executive Andy Mitchell told the Financial Times he was confident the company was delivering the project in the most timely and cost-efficient way.
He said: “We will continue to get on with providing London with this much-needed piece of infrastructure.”
The Department For The Environment, Food And Rural Affairs said the project was needed to “modernise the capital’s ageing sewage system”.
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