A spokesman said on Friday the prosecutor's office suspected that the president was also guilty of wrongdoing, but he was protected from prosecution as long as he was in office.
Chang Wen-cheng, the spokesman, said: "The High Court prosecutor has determined that President Chen is involved with the crimes of corruption and faking of documents, but this part of the case is subject to guarantees provided under ... the constitution and we must wait until the president is recalled or finishes his term before we can pursue further investigation".
The High Court will charge Wu Shu-chen, the president's wife, with corruption, faking evidence and faking documents in a case involving the misuse of more than $448,500.
Wu has previously denied any wrongdoing.
The prosecutor also plans to file charges against others including Ma Yong-cheng, a former close aide to Chen, according to a statement by the prosecutor's office.
"The High Court prosecutor has determined that President Chen is involved with the crimes of corruption and faking of documents"
spokesman of the prosecutor's office
The filing of charges stems from a case involving Chen and those around him, and their possible under-documented use of funds from a special state affairs budget.
The investigations against Chen and Wu, along with an unrelated investigation and charges against their son-in-law, Chao Chien-ming, have weighed on his administration since this spring, leading to a movement calling for Chen's removal.
Chen's popularity has sunk to new lows since the series of investigations emerged.
In an attempt to placate critics, Chen ceded some powers in June to Su Tseng-chang, the prime minister.