Preliminary data released by the health ministry showed 19,959 people died by suicide in 2019, a 4.2 percent drop for the country of 127 million people. Seventy percent of those were men.
Final data will be released in March, and the figures are likely to be slightly higher, after police confirm whether deaths recorded in the final months of the year were linked to suicide.
But officials said the final figure was still expected to be a record low since data collection began in 1978.
The numbers are declining "thanks to increasing efforts to prevent suicide, since the issue has been recognised as social issue" rather than an individual problem, Yasuyuki Shimizu, who heads nonprofit suicide prevention group LIFELINK, told AFP.
Government efforts, including enacting a suicide prevention law and starting anti-suicide campaigns, have paid off, he said.
"The number declined, but the people who died will not come back... it's not normal that about 20,000 still die every year," Shimizu warned.
The number of suicides in Japan peaked in 2003 at 34,427 and the figure remained above 30,000 between 2004 and 2011, but has been falling steadily since then.
The latest government data did not include reasons for suicide cases, but last year the ministry cited multiple factors including financial issues, overwork, family problems, and depression.
Health Minister Katsunobu Kato told reporters on Friday that Japan "must face the fact that 20,000 people still took their own precious lives."
"We want to continue efforts, such as by using social media, to create a society in which no one is pushed into suicide," he said.
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