The National Intelligence Service (NIS) took United Progressive Party (UPP) legislator Lee Seok-Ki away from his office in parliament after a confrontation with his supporters.
Scuffles erupted as UPP members blocked dozens of NIS agents at the office door.
Police eventually stepped in to end the noisy stand-off which lasted for nearly one hour. Television showed Lee surrendering and walking out.
Some exhausted UPP members fell to the ground or screamed as the NIS agents escorted Lee out.
He will be held at the court, which had issued a warrant for his detention, pending his formal arrest by state prosecutors.
Rival political parties earlier joined forces to approve Lee's arrest on sedition charges. Without such a vote, lawmakers cannot be detained while the legislature is in session.
Some 258 legislators voted for the arrest while 14 objected.
Hundreds of police, including riot officers carrying shields, had stood guard outside the National Assembly as the vote was under way, with riot vans blocking roads and a water cannon atop an armoured vehicle.
Justice Minister Hwang Kyo-Ahn told lawmakers that in May Lee -- believing war with the North to be imminent -- told his secretive leftist group to prepare for attacks on South Korea's communication lines and railways.
Lee replied that he was the victim of a "savage and irrational witch hunt" led by the country's secret police and fanned by the conservative news media.
"They may jail me for a while but steps towards independence, peace and democracy will never falter," Lee told parliament.
"We'll never tolerate anyone who is willing to fight on the side of the enemy in the event of a war," said Democratic Party chief Kim Han-Gil.
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