Over the past several months Chen has been facing increasingly pointed opposition charges that he and his administration have fostered an atmosphere of rampant corruption around the Presidential Office.
Prosecutor Tzeng Yi-sheng told The Associated Press he questioned Wu Shu-chen for three hours at National Taiwan University Hospital in Taipei on Sunday.
The wheelchair-bound Wu is reportedly in poor health.
However, Taipei Prosecutor's Office spokesman Lin Pang-liang refused to characterize Wu as a suspect in the probe into the store's affairs.
Opposition lawmakers have charged that Wu received free vouchers from the Sogo Department Store, and may have played a role in its takeover by a businessman whose bid was less than that of at least one rival suitor.
The Presidential Office has denied the charges, the AP reports.
Wu has not made any public appearances since the Sogo affair broke in April. She remained secluded on Tuesday, her 55th birthday, despite her past practice of appearing in public to mark the event.
She has been paralyzed from the waist down since a truck ran over her in 1985, just as Chen and his allies were struggling to break the monopoly grip on power of Taiwan's once dominant Nationalist Party, now the leading opposition voice.
Chen has called the incident an assassination attempt and blamed the Nationalists for carrying it out.