President Yoon Suk Yeol imposed martial law late Tuesday and sent armed forces to the National Assembly. The measure was canceled six hours later, after the parliament voted against it.
Kim, who allegedly played a key role in proposing and implementing the emergency decree, was placed in emergency custody at around 1:30 a.m., the special investigation unit said.
Kim faces charges of insurrection and abuse of authority.
He voluntarily appeared at the Seoul Central District Prosecutors' Office for questioning late Saturday night.
The arrest came a day after a motion to impeach Yoon was scrapped due to a lack of quorum after the ruling People Power Party (PPP) boycotted the vote.
Prosecutors are expected to seek a formal arrest warrant for Kim within the next 48 hours, as required by law.
On Thursday, prosecutors imposed a travel ban on Kim following his resignation.
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