A Kuala Lumpur court found Ling Liong Sik not guilty of cheating the government over the Port Klang Free Trade Zone, a huge 1,000-acre commercial and industrial project south of the capital.
Local media reports said the judge acquitted Ling on the charges of deceiving the government in 2002 over a land purchase for the project. Ling was transport minister from 1986 to 2003.
Ling's lawyer Wong Kian Kheong confirmed the acquittal but declined to comment further. Prosecutors, who can appeal the verdict to a higher court, did not immediately return a request for comment.
"The old habits of the regime have been restored... It's not a very encouraging sign," Chua said, adding the acquittal sent a message to Malaysia's ruling elite that "their interests will not be jeopardised".
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Local media reported that the project's initial cost of 1.1 billion ringgit (USD 350 million) spiralled to more than 4.6 billion ringgit.
Besides Ling, a few others have also been charged, including another former transport minister whose trial has not been concluded.
Corruption -- from small bribes for minor traffic offences to huge contracts awarded without transparent tender -- is endemic in Malaysia. Successful high-profile prosecutions are rare.
In August, a court overturned a 2009 murder conviction for two police officers in the killing of a Mongolian woman, a 28-year-old model and interpreter at the centre of allegations of huge kickbacks in a government purchase of French submarines.
Critics have tried to link the case to the premier, who was defence minister at the time of the USD 1.1-billion purchase of the submarines in 2002. Najib has denied any wrongdoing.