The Baltic Dry Index, a measure of shipping costs for commodities, dropped 3.1 percent Wednesday, the first decline since Aug. 4 and as such shipping lines in Japan declined.
Mitsui O.S.K. lost 1.1 percent to 536 yen after the company's stock was lowered to "underperform" from "outperform" by Mizuho Securities.
Counterpart Nippon Yusen K.K., the country's biggest shipping line by sales, sank 1.2 percent to 331 yen and Kawasaki Kisen Kaisha Ltd., retreated 0.9 percent to 323 yen.
Parco Co. was a notable advancer on Thursday, surging 5.2 percent to 646 yen. The manager of shopping centers will sell 15 billion yen (177.33 million U.S. dollars) of convertible bonds to the Development Bank of Japan, according to a filing with the finance ministry.
Separately, Parco announced the company will expand its business in China.
Some 1.41 billion shares changed hands on the Tokyo exchange's First section, down from Wednesday's volume of around 1.78 billion, with advancing issues outnumbering declining ones by 1,053 to 439.