In 2006, he and his family were targeted by the Seoul Supreme Prosecutor's Office as part of an investigation into embezzling 100 billion won ($106 million) from Hyundai to create slush funds to bribe officials. Despite a travel ban, Chung left South Korea in April 2006. Chung was arrested on 28 April 2006 on charges related to embezzlement and other corruption.

On 5 February 2007 he was convicted of embezzlement and breach of fiduciary duty for selling securities to his son Chung Eui-sun at below-market prices. He was sentenced to three years in prison. Chung remained free on bail while he appealed the sentence. On September 6, 2007, Chief Judge Lee Jae-hong ruled to suspend the sentence of Chung Mong-koo (in consideration of the huge economic impact of imprisonment), ordering instead of a 3-year jail term, community Service and a $1 billion donation to charity.

The trial was seen as "a victory for transparency and rule of law in South Korea", but on August 15, 2008, South Korean President Lee Myung-bak granted him a special pardon to allow Chung to continue to contribute to the development of Hyundai Motor Group as well as the Korean economy.

Furthermore, in 2011, he was accused of nepotism when Ozen, a bakery cafe whose advisors included his three daughters Sung-yi, Myung-yi, and Yun-yi, set up shop in company buildings. Ozen eventually closed in 2012.

As of March 2014, his net worth was $6.8 billion according to Forbes.

Although he only holds 5.2% of Hyundai Motor’s stock, Chung "wields disproportionately strong control" and is able to control its board thanks to a complex corporate governance arrangements in which Hyundai Motor owns 34% of Kia, which owns 16.9% of Mobis, which in turn owns 20.8% of Hyundai Motor. This means that "because the companies essentially control each other, no outside shareholder is strong enough to name board members".