The approval is the first step in launching a full investigation into the allegations, Yonhap News Agency reported.
Rep. Lee Seok-ki, of the Unified Progressive Party, is facing charges of leading a secret organization with suspected links to North Korea.
The group allegedly planned to destroy South Korean infrastructure, including communication lines and railways, in the event of a war with North Korea, Yonhap said.
Lee has denied the allegations and protested the Assembly's consideration of the motion.
"It would be an indelible mistake for the National Assembly to go along with a fabricated rebellion conspiracy, which [I] will be acquitted of in just a few months time," Lee said in his address to the Assembly ahead of the vote.
The Assembly approved the arrest by a margin of 258-14.
The motion was filed with the National Assembly Monday, after prosecutors requested to detain Lee for questioning.
Parliamentary consent is necessary for the arrest of lawmakers while the assembly is in session.
He has previously been jailed for pro-North Korean activities, Yonhap said.
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