Son Kil-Seung is accused of drawing more than $667 million from the group without the permission of company directors for overseas futures investment.
He and six others are also accused of diverting more than $30 million in taxes.
Prosecutors are investigating claims Son provided funds to politicians in 2002 ahead of elections.
"The accused is expected to receive severe punishment," a senior judge at the Seoul district court said on Saturday in a statement given as reasons for the court allowing Son's arrest.
On Friday, Chyung Dai-chul, a senior aide to the South Korean President Roh Moo-hyun, was arrested on charges of bribery and illegally financing a political campaign.
Five other opposition party lawmakers were also arrested on Saturday.
The six, and Son, are all implicated in the violation of political funding laws, prosecutors say.
More arrest warrants were being sought for other lawmakers alleged to have diverted funds into the campaigns of president Roh Moo-Hyun and his conservative opponent during the 2002 presidential election cycle