Former lawmaker Lee Sang-deuk faces allegations of taking 600 million won (£338,200;$525,000) in bribes from the chairmen of two savings banks to help them avoid an audit.
The arrest warrant was approved by the Seoul Central District Court.
It is seen as a potential political setback for South Korea's conservative ruling party in an election year.
The presidential election takes place in December.
As Lee Sang-deuk arrived in court, angry depositors who lost money when the savings banks were suspended hurled eggs at him.
The 76-year-old, who served six terms in parliament, was reportedly taken to a detention centre immediately after the warrant was issued.