The Port Klang Free Trade Zone, a commercial and industrial project south of the capital, was conceived as a 1.82 billion ringgit (539 million dollar) venture constructed over 1,000 acres (405 hectares).
However costs are now expected to balloon to 12.5 billion ringgit, making the affair one of the country's biggest financial scandals and a major embarrassment for the government.
A report by the Port Klang Free Trade Zone's external auditors has indicated it would be loss-making until 2029 because of debt servicing costs, and would only break even in 2051.
Prosecutor Manoj Kurup said that O.C. Phang, the former head of the Port Klang Authority which runs the zone, had been charged at the Klang Sessions Court with three counts of criminal breach of trust.
She denied the allegations over payments worth 254 million ringgit to the project's developer. She faces 20 years in jail if convicted.
Two other individuals, the chief executive of the developer and a consultant architect, also denied charges of cheating in relation to an amount of 122 million ringgit, the prosecutor said.
"They were charged for basically certifying work done when that work had not been done, and as a result of their certification the port authority paid out the money," he said.
The pair face up to 10 years in jail if found guilty.