It was the latest blow in a scandal that has led to mass protests and calls for the president's removal.
A statement from the prosecutor's office said the high court would charge First Lady Wu Shu-chen with corruption and faking documents in a case involving the misuse of more than T$14.8 million ($448,000).
The prosecutor's office also mentioned allegations of perjury, but it was unclear whether charges on that count were filed against Wu.
It said Chen himself might also be guilty of wrongdoing in the case, but that he was immune from prosecution until the end of his tenure, which is due to run until 2008.
"In the end it was determined through receipts of purchases by other people, that Wu Shu-chen between July 2002 and March 2006 embezzled over T$14.8 million of non-secret state funds," Chang Wen-cheng, spokesman for the high court prosecutor's office, told a news conference.
"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," he said.

"RESIGN" CALLS
The main opposition Nationalist Party (KMT) called on Chen to step down, joining protesters who have been demanding his resignation in a series of major street demonstrations attracting hundreds of thousands of people.
"President Chen has lost the respect and trust of the Taiwan people," said KMT chairman Ma Ying-jeou. "We urge President Chen Shui-bian to step down as soon as possible ... We urge the ruling party to show courage and strength in getting President Chen to step down immediately."
A spokesman at the president's office had no immediate comment.
Wu and Chen have denied any wrongdoing. Chen's Democratic Progessive Party called a meeting for later in the evening, but had no immediate comment.
The president was unlikely to step down, at least for now, said Andrew Yang, secretary-general of the Chinese Council of Advanced Policy Studies.
"But it really depends how much pressure he faces from his opponents and from his own party," Yang said. "This has further damaged his leadership and credibility and will create more resentment from those against him and add more challenges for the DPP."
The investigations against Chen and Wu, and an unrelated investigation and charges against their son-in-law, Chao Chien-ming, have weighed on his administration this year and dragged the president's popularity to new lows.
In a bid to placate his critics, Chen ceded some powers in June to Premier Su Tseng-chang. The transfer gave Su "full power to decide and be completely responsible for all cabinet policies in the future", Chen said at the time.
Traders took the long-awaited news, which came after the market closed, in their stride, saying they expected only a limited short-term impact.

Copyright Reuters, 2006