Yoon said Wednesday he complied with investigators to avoid “bloodshed” but did not accept the legality of the investigation.
Meanwhile, officials were trying to secure a new warrant that could hold him for longer than 48 hours.
South Korea’s opposition Democratic Party celebrated Yoon’s detention, while the parliament speaker said it was time to stabilise the country after weeks of turmoil.
Yoon’s lawyers have instead filed for a review of the warrant that was used to arrest him.
Trial tribulations
Yoon shocked the nation late on December 3 when he declared martial law, claiming he needed to safeguard South Korea “from the threats posed by North Korea’s communist forces and eliminate anti-state elements”.
The 64-year-old suspended leader then sought to evade arrest for weeks by remaining in his residential compound, protected by loyal members of the Presidential Security Service (PSS).
He remained defiant Wednesday after his arrest, publishing on Facebook what he said were his writings from inside the residence, repeating unproven claims of election fraud.
Shortly after he was taken to the CIO offices in a convoy, investigators began questioning Yoon but they said later he exercised “his right to remain silent”.
His supporters have also refused to accept the arrest.
During the hours-long standoff between police and Yoon’s guards, they chanted “illegal warrant!” while some laid on the ground outside the main gate of his residence.
In a parallel probe, the Constitutional Court is deciding whether to uphold parliament’s impeachment of Yoon.