Kwon Yun-Ja, 72, was arrested at a flat in the southern suburbs of Seoul following a successful ambush, Yonhap news agency said.
But her husband Yoo Byun-Eun, 73, was not at the site.
YTN TV showed Kwon, her face covered with a dark brimmed hat, being taken into custody at the Incheon Prosecutor's Office.
Investigators want to question her to obtain information that may lead to the capture of her husband.
Yoo is the patriarch of the family behind Chonghaejin Marine Co, which owned and operated the 6,825-tonne Sewol ferry which sank on April 16 with the loss of around 300 lives, most of them schoolchildren.
Yoo has no direct stake in Chonghaejin, but his children and close aides control it through a complex web of holding companies.
His wife Kwon was accused of diverting funds from one of Chonghaejin's subsidiaries where she serves as the CEO.
A reward of 500 million won (USD 490,000) has been offered for information leading to the capture of Yoo and 100 million won for that of his eldest son, Yoo Dae-Kyun.
Several church followers suspected of helping Yoo evade a nationwide dragnet have also been arrested after he defied an official summons to surrender to prosecutors.
