Chun was ordered in 1997 to return $19.7 million a court found he had illegally accumulated during his administration, but Chun said he was unable to pay because he was nearly penniless, Yonhap news agency reported.
The ex-president has since paid some of the fine but $15 million is still outstanding.
A number of properties, including what were described as expensive works of art, were seized during the raid, which was conducted by nearly 90 investigators with the Seoul Central Prosecutor's Office and the National Tax Service.
Investigators also raided the headquarters of 17 firms, including two owned by Chun's oldest son, suspected of concealing the former president's assets.
The raid was spurred by the approach of the expiration in October of the statute of limitation in Chun's case.
South Korean lawmakers in June passed a bill extending from three years to 10 the time in which public officials have to pay fines. Chun now has until 2020 to pay the remainder of his fines.