The deficit narrowed by 12.9 percent from the same period last year when it ballooned to the largest ever for the period, according to the Finance Ministry.
In the first six months, the country's imports edged up 0.7 percent, while exports gained 3.1 percent, the preliminary report showed.
Thursday's data also showed that Japan posted a 43 billion yen (300 million U.S. dollars) trade surplus in June, returning to the black for the first time since July 2021.
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