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.
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".