"The market was supported a bit by bargain-hunting. But cheap valuations alone would not be enough for buying. The market will be capped unless we see positive headlines on coronavirus," said Masahiro Ichikawa, senior strategist at Sumitomo Mitsui DS Asset Management.
Positive news on the virus was in short supply, with both China and South Korea reporting 500 new cases, while there are signs of fresh outbreak in other countries such as Thailand and Bahrain.
Adding to the fears was an alert from the US Centers for Disease Control and Prevention on Tuesday warning Americans to prepare for the spread of coronavirus in the United States, signalling a change in tone for the Atlanta-based US health agency.
The broader Topix lost 0.75% to 1,708.89 in active trade, with turnover hitting more than 3 trillion yen for two sessions in a row.
All of the 33 sector sub-indexes on the Tokyo Stock Exchange were trading lower, with mining, real estate and services being the worst three performers.
Mitsubishi Estate Co Ltd closed 2.8% lower after Bloomberg News reported a person infected with the new coronavirus had been at Shin Marunouchi Building, one of the landmark buildings that the company developed in Tokyo's premier business district.
The virus has also hit some Olympics-related stocks on mounting worries it could lead to cancellation of the 2020 Summer Games scheduled to start in Tokyo in July.
Dentsu Group Inc dropped 0.7%, sliding for a sixth day to a seven-year low, amid concerns the Tokyo Olympics will be cancelled and hurt Japan's largest ad agency.
Other Olympic-related shares also plummeted. Hibino, which provides audio and visual services at big events, closed 7.4% weaker, while sportswear maker Mizuno lost 2.4% to a one-year low.
Event organising service firms were battered after Prime Minister Shinzo Abe called for sports and cultural events to be scrapped or curtailed for two weeks.
TKP lost 3.9%, while Hakuten ended down 6.4%.
The Nikkei's volatility index, a measure of investors' volatility expectations based on option pricing, spiked to as high as 29.74, its highest level in 14 months.