Investors were closing their positions after a national holiday on Thursday and ahead of an extended weekend that will see the market closed from Monday until Wednesday. Normal trading will resume from Thursday.
"In early trade, selling related to position adjustments ahead of the holiday period are dominating the market, rather than the market reflecting strong US shares," Okasan Online Securities said.
On Wall Street, the Dow finished up 0.7 percent, as did the S&P 500. The tech-rich Nasdaq rose 0.2 percent.
The Tokyo market remained well supported following the US Federal Open Market Committee's latest meeting, while investors digested the Biden administration's policy announcement, analysts said.
Worries over the Olympics were also weighing on the Tokyo market.
"There are lingering speculations about the possible cancellation of the Olympics, which make Japanese shares unattractive to buy," Okasan said.
The Tokyo Games are scheduled to open on July 23, but the capital and other economic hubs in Japan are seeing a fresh surge in coronavirus cases.
Hospitals in the western city of Osaka are struggling to cope with the spike in infections, and Japan's government has imposed a state of emergency for the city and its surrounding areas, as well as in Tokyo.
Doctors and medical experts are increasingly speaking out against holding the pandemic-postponed Games, while polls have long suggested that the public largely support a cancellation or a delay.
The dollar stood at 108.89 yen, little changed from 108.92 yen in New York overnight.
The government said Japan's factory output in March rose 2.2 percent from the previous month.
Among major shares, Sony Group plunged 5.67 percent to 11,140 yen. Chipmaker Murata Manufacturing dropped 3.17 percent to 8,737 yen, and Toyota lost 1.16 percent to 8,203 yen.
But SoftBank Group firmed 0.93 percent to 9,983 yen. Medical equipment maker Olympus added 0.27 percent to 2,255.5 yen. Nintendo rose 0.74 percent to 62,710 yen.
This story has been published from a wire agency feed without modifications to the text. Only the headline has been changed.
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