While analysts expected export growth to slow from a sharp rebound in the first quarter, the yen's recent gains and signs of a slowdown in big markets such as the United States and China have heightened uncertainty on the outlook for Japan's export-reliant economy.
Exports rose 27.7 percent in June from a year earlier, more than a median market forecast for a 23.5 percent increase, trade data from the Ministry of Finance showed on Monday.
But export growth slowed for the fourth straight month after peaking in February, when it rose 45.3 percent, boding ill for an economy heavily reliant on overseas demand. From May, exports were down 1.8 percent, the second consecutive drop on a month-on-month basis.
Shipments to Asia, which account for more than half of Japan's total exports, rose 31.7 percent in June from a year earlier but that still represented a slowing for the fifth straight month.
Exports to China rose 22.0 percent from a year earlier, also marking the fifth straight month of slowdown.
The slowdown was particularly noticeable in shipments to the European Union, with growth shrinking to 9.0 percent from 17.4 percent in May, as the yen's rise against the euro and the region's debt crisis hurt automobile demand, a MOF official said.
But exports to the United States picked up on brisk auto shipments, as the yen's rise against the dollar had been relatively gradual.
The real exports index compiled by the Bank of Japan, used to assess changes in export volume, edged down 0.4 percent to mark its first drop in 16 months, but the degree of fall was modest compared to strong rises in preceding months, indicating export volumes have held relatively steady.