A body believed to be Hideaki Noguchi, vice president of H S Securities Co, was found in a hotel in the southern prefecture (state) of Okinawa on Wednesday evening, according to local police spokesman Tatsuki Yara.
Police suspect that Noguchi, 38, committed suicide, Yara said.
HS Securities is among the companies raided this week by prosecutors in connection with fraudulent practices by Livedoor, according to Kyodo News agency.
Officials at the securities firm refused to confirm the report.
Internet company Livedoor is facing a widening criminal investigation that had sparked a massive sell-off in Japan's stocks market on Tuesday and Wednesday. The market recovered on Thursday.