TOKYO--Japanese exports rebounded in September, growing 6.9% from a year earlier, the finance ministry said Wednesday, helped by the yen's descent in the reporting month and a surge in output among suppliers of Apple Inc.'s new smartphones.

But the nation's trade deficit still edged up 1.6% to Y958.3 billion from a year earlier, the first increase in three months. That compared with a median forecast for a Y768 billion deficit in a survey of economists by The Wall Street Journal and the Nikkei.

While a weaker yen helps inflate the value of Japan's exports it also increases the bill for imports, which rose 6.2% in September. A large increase in natural gas imports also pushed up the import figure, ministry data showed.

In September, the Japanese currency fell to a six-year low close to Y110 to the dollar.

The record 27th straight monthly trade shortfall comes amid a severe shortage of manual labor in Japan and continued off-shoring by Japanese multinationals--a trend that some economists say gives Prime Minister Shinzo Abe's efforts to boost the economy through a weaker yen may only a limited effect.

The lengthy deficit run also reflects Japan's energy woes. The nation's nuclear power plants have been kept off-line as a result of the 2011 Fukushima nuclear accident, leaving the country reliant on fossil fuel for 90% of electricity generation, up from around 60% prior to the accident.

Japan's trade data followed upbeat trade figures from China and South Korea earlier in the month. For the month of September, China reported a 15% jump in exports and a 7% rise in imports. South Korea said its exports and imports grew 7% and 8%, respectively. Both countries import Japanese electronics components and produce smartphones and other electronics devices for exports worldwide.

The global outlook remains far from rosy, however. Earlier this month, the International Monetary Fund reduced its global growth forecast to 3.8% from 4.0% for 2015, compared with 3.3% growth projected for this year, amid sluggish growth in the eurozone and Japan.

Write to Mitsuru Obe at mitsuru.obe@wsj.com

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