Chen and family members have been accused of laundering millions of US dollars by sending political donations and secret diplomatic funds abroad, as well as taking kickbacks on government contracts and bribes from businessmen during his 2000-2008 presidency.
Among the cases, Chen was convicted of taking around $6.74 million in bribes paid by Yuanta Securities to facilitate its merger with another company in a final ruling in 2012.
Taiwan in 2013 requested Switzerland return the money which had been frozen in Swiss bank accounts in the names of Chen's son and daughter-in-law, although the couple contested the move in Swiss courts, according to Taiwan's supreme prosecutor's office.
"We were notified by Swiss prosecutors that the Swiss Supreme Court has ruled that the fund in connection to the Yuanta financial merger case will be returned to Taiwan soon," said Kuo Wen-dong, a spokesman for the special investigation unit under the office.
Swiss authorities have already returned to Taiwan around $22 million in deposits held by Chen following his corruption conviction in several other cases, according to the office.
Chen, who had been serving a 20-year jail term on multiple graft and money laundering convictions relating to his time in office, was released on medical parole early January after being diagnosed with severe depression, suspected Parkinson's disease and other conditions.
The 64-year-old was originally sentenced to life in prison in 2009 but the term was reduced to 20 years after appeals.
Chen's wife Wu Shu-chen, who is paralysed from the waist down and confined to a wheelchair, has been spared from serving a 20-year sentence handed down for her role in the corruption offences due to poor health.
Chen insists that the charges against him are part of a politically motivated vendetta by the current Beijing-friendly Kuomintang government, in retaliation for his years in power when he promoted the idea of Taiwan declaring independence from China.
Under its "One China" policy, Switzerland does not recognize Taiwan, also known as the Republic of China, as an independent state and does not have any official contacts with the country.
However, Switzerland has significant trade with Taiwan, which is pursued through private channels.