The 225-issue Nikkei Stock Average lost 250.67 points, or 0.90 percent, from Thursday to close the day at 27,522.26.
The broader Topix index of all First Section issues on the Tokyo Stock Exchange, meanwhile, dropped 11.35 points, or 0.59 percent, to finish at 1,927.18.
Local brokers said that Japan's expansion of its COVID-19 quasi-state of emergency to more prefectures stoked concerns over the future health of Japan's economy.
Currently, there are 16 prefectures under the quasi-state of emergency with more to follow suit henceforth. This follows Hiroshima, Yamaguchi and Okinawa being placed under the measure from Jan. 9 after virus outbreaks at U.S. military bases there.
On Thursday, Japan reported more than 46,000 new daily infections, marking a new national record for the third straight day.
After the closing bell Friday, Tokyo reported 9,699 new cases, also a new record and far surpassing the previous record logged a day earlier at 8,638 new infections.
"Investors are concerned that the recent surge in infections will stall economic recovery as manufacturers such as Toyota Motor have been forced to temporarily close factories," Yutaka Miura, senior technical analyst at Mizuho Securities Co., was quoted as saying.
Investor sentiment was also dampened by the tech-heavy Nasdaq index sliding overnight and dragging down their counterparts here.
"The market tracked Wall Street and chip-related shares that became a target of a sell-off after the Nasdaq's losses," Kazuharu Konishi, head of equities at Mitsubishi UFJ Kokusai Asset Management, said.
By the close of play, mining, transportation equipment, and oil and coal product issues comprised those that declined the most, and issues that rose outpaced those that fell by 1,170 to 920 on the First Section, while 94 ended the day unchanged.
Among issues losing ground on virus-related issues, Toyota Motor fell 2.5 percent as 11 factories in Japan may be suspended for three days this month due to supply chain bottlenecks caused by a resurgence of the the COVID-19 pandemic and workers becoming infected, the automaker said.
Some export-linked issues weighed on the market owing to the yen's rise against the U.S. dollar, with Mitsubishi Motors dropping 3.7 percent, while Mazda Motor lost 3.4 percent by the close.
Tech shares followed their U.S. peers lower, with Shin-Etsu Chemical retreating 2.5 percent, Advantest losing 4.2 percent, while Tokyo Electron slumped 6.3 percent.
TDK closed down 2.0 percent and Kyocera slipped 0.8 percent.
On the main section on Friday, 1,235.00 million shares changed hands, dropping from Thursday's volume of 1,282.47 million shares.
The turnover on the final trading day of the week came to 2,987.39 billion yen (26.20 billion U.S. dollars).
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