Prison authorities, meanwhile, said the country's former defence minister tried to kill himself shortly before his formal arrest over the events of the night of December 3.
The extraordinary drama saw troops and helicopters sent to parliament in an apparent -- but failed -- attempt to prevent lawmakers from voting down Yoon's martial law declaration.
The deeply unpopular Yoon is already under a travel ban as part of an "insurrection" probe into his inner circle.
On Wednesday, a special investigation unit of South Korea's police said it raided the presidential office as well as the National Police Agency, the Seoul Metropolitan Police Agency and the National Assembly Security Service.
A statement gave no further details.
Former defence minister Kim Yong-hyun tried to kill himself shortly before midnight on Tuesday (1500 GMT Tuesday) while in custody, authorities said.
Kim was first detained on Sunday. The suicide attempt took place shortly before he was formally arrested, the justice ministry and a prison official said.
They added that he was in good health on Wednesday.
Kim was arrested on charges of "engaging in critical duties during an insurrection" and "abuse of authority to obstruct the exercise of rights".
The former defence minister said through his lawyers that "all responsibility for this situation lies solely with me" and that subordinates were "merely following my orders and fulfilling their assigned duties".
He had already been slapped with a travel ban along with the former interior minister and the general in charge of the martial law operation.
Cho Ji-ho, commissioner general of the Korean National Police Agency, and Kim Bong-sik, head of the Seoul Metropolitan Police Agency, were also arrested early Wednesday, police said.
'Fascist dictatorship'
North Korean state media on Wednesday made its first comments about what it called the "chaos" in the South.
"The shocking incident of the puppet Yoon Suk Yeol, who is facing impeachment and a governance crisis, suddenly declaring a martial law decree and unhesitatingly wielding the guns and knives of its fascist dictatorship wrought chaos across South Korea," a commentary said.
Yoon had said his declaration of martial law was intended, in part, to safeguard South Korea "from the threats posed by North Korea's communist forces and eliminate anti-state elements plundering people's freedom and happiness".
Relations between the two Koreas have been at one of their lowest points in years, with the North launching a flurry of ballistic missiles in violation of UN sanctions.
Former defence minister Kim had been accused by opposition lawmakers of calling for strikes on sites from which North Korea was launching trash-carrying balloons, an order reportedly refused by his subordinates.
He also allegedly ordered drones sent to the North Korean capital of Pyongyang in an apparent attempt to provoke a conflict as a pretext for declaring martial law.
Task force
Yoon survived an impeachment motion in parliament on Saturday even as tens of thousands of South Koreans braved freezing temperatures to demand his ouster.
Further smaller protests have continued every evening since, with polls showing record-low public support for Yoon.
A special task force within Yoon's People Power Party (PPP) on Tuesday proposed a plan for the president to resign in February or March, followed by fresh elections in April or May.
But the proposal has not yet been adopted by the party as a whole.
Even if approved, the roadmap is unlikely to head off another opposition attempt to impeach Yoon on Saturday.
The motion only needs eight members of Yoon's People Power Party (PPP) to secure the necessary two-thirds majority.
Last week, two PPP lawmakers -- Ahn Cheol-soo and Kim Yea-ji -- voted in favour, and two more said Tuesday they would support the motion this time.
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