Among individual companies, Target slumped 6.8 percent despite reporting a 66 percent jump in fourth-quarter income to $1.4 billion on another round of surging sales amid the coronavirus pandemic.
Toshiba, which returned to the prestigious first section of the Tokyo Stock Exchange on Friday more than three years after it was demoted to the second section, was trading down 0.87 percent at 3,400 yen.
Short-seller Citron, a target for some of the individual traders who have helped drive huge gains for a number of niche Wall Street stocks in the past week.
GameStop's stock has surged nearly 700% in the past two weeks, upping the struggling video retailer's market value from $1.24 billion to more than $10 billion.
All three major indices ended at records Wednesday after Joe Biden was sworn in as president amid optimism over the new administration's plans to support the US economy and improve the Covid-19 vaccine rollout.
Japan has booked a trade surplus of 366.8 billion yen ($3.5 billion) in November, the fifth consecutive monthly surplus, according to data released by the finance ministry before the opening bell, which prompted little reaction from investors.
Among major shares in Tokyo, shipping firms were down, with Nippon Yusen declining 1.13 percent to 2,367 yen, Mitsui O.S.K. Lines dropping 0.57 percent to 2,975 yen, and Kawasaki Kisen down 2.37 percent at 1,939 yen.