Kim has been accused of ordering an early end to a government inquiry into the North Koreans captured near the inter-Korean sea border and sending them back to the North despite their wish to defect to South Korea, while he was unification minister.
The North Koreans' repatriation is one of the two suspicious cases involving the former Moon Jae-in administration that President Yoon Suk-yeol's government is revisiting, along with the North's killing of a South Korean fisheries official near the western sea border in 2020.
The Moon administration was accused of mishandling the two cases in an attempt to curry favor with Pyongyang so as to move the stalled inter-Korean peace process forward.
The North Koreans had expressed a desire to defect, but the Moon administration determined their intentions as insincere and repatriated them, citing their confessions to having killed 16 fellow crew members.
The Seoul Central District Prosecutors Office questioned Kim as an accused on Tuesday, officials said.
Also on the day, prosecutors questioned Kim Joon-hwan, a former senior official at the National Intelligence Service, who has been accused of fabricating an official report involving the repatriation. (Yonhap)