Chen and Wu are also accused of laundering part of their alleged ill-gotten wealth by wiring the money to Swiss bank accounts.
More than 10 former aides and family members, including the Chens' son and daughter-in-law, are also facing similar charges in connection to suspected financial crimes that prosecutors say involve a total of about $27m.
Chen, who could be jailed for life if convicted on all charges, denies any wrongdoing.
Al Jazeera's David Hawkins, reporting from Taipei, said Chen was claiming that his prosecution was really political persecution by the ruling Kuomintang party who took over from his Democratic Progressive party.
In November, Chen went on a hunger strike to protest against his arrest and was later hospitalised for irregular heartbeat caused by slow metabolism.
The trial has divided Taiwan and has deepened differences between those who support a more pro-independence stance as Chen does, and those who seek warmer ties with China as Ma Ying-jeou, Chen's successor, does, our correspondent said.
Taiwan has been a self-governed island since the Kuomintang army fled there after losing the Chinese civil war to the communists in 1949.
China, which still considers Taiwan a renegade province and has threatened to use force to quell any move towards formal independence, often bristled at Chen's independence moves.
The two countries have enjoyed a thawing of relations since Ma won elections last year on a platform of having closer economic ties with Beijing.