A special team of investigators stormed the office in Geoje Island near the southern city of Busan earlier in the day and seized computer files, documents and account books, the Seoul Central Prosecutors' Office said.
Prosecutors declined to identify the company, only saying that it provides ship parts to DSME, South Korea's second-largest shipyard.
Prosecutors said they were tipped off that the company pocketed tens of billions of won between 2004 and 2008 in the process of making construction project deals with the DSME.
The central investigation department of the office will also look into allegations that Daewoo Shipbuilding Chief Executive Nam Sang-tae used part of the secret fund in lobbying for his re-election bid for chief of the company, officials said.