That followed the downwardly revised 638.6 billion yen deficit in May (originally a 637.6 billion yen shortfall).
Exports were down 0.5 percent on year, missing forecasts for a gain of 0.5 percent after sinking 1.7 percent in the previous month.
Imports rose an annual 0.2 percent versus expectations for a drop of 1.6 percent after losing 7.7 percent a month earlier.
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