The Seoul Central District Court issued the arrest warrant for Lee Sang-deuk, the elder brother of President Lee Myung-bak, late on Tuesday.
Hours earlier, as the suspect entered the court for questioning, enraged protesters threw eggs at him, grabbed his tie and jostled him.
Lee was taken early on Wednesday from the prosecutors' office to the Seoul Detention Centre, according to an official who declined to provide further details, including his name, citing office rules.
As he left the prosecutors' office, Lee said he was "sorry" when asked by a reporter if I had anything to say to the country's president and the South Korean people.
The former lawmaker is accused of taking half-a-million dollars in bribes from two detained bankers with the intent of using his influence to help the bankers avoid punishment.
Lee Myung-bak ends his single, five-year presidential term early next year.
Elections for the next president are in December.