China's National Audit Office says some 2 billion yuan (USD 314 million) remains unaccounted for in connection with an underground hydro-electric plant worth around 7-billion yuan (USD 1.11 billion).
It follows a critical report released last year that found nepotism and other corrupt practices in the construction of the dam, state-run People's Daily reported today.
The Three Gorges Corporation, which runs the dam, claims all the problems pointed out by the audit have been rectified.
The Three Gorges Dam on Yangtze River is the world's largest power station in terms of installed capacity (22,500 MW) and it has been controversial almost since construction first began in 1994.
Environmental groups had warned of risks of ecological disasters and over a million residents had to be relocated for the construction.