Import costs in Japan have largely been driven by strong demand for fossil fuels to make up for the nuclear power lost since the Fukushima nuclear crisis that followed the 2011 earthhquake and tsunami.
The weaker-than-expected export numbers from Japan follow disappointing economic growth data earlier this week that has cast a cloud over Prime Minister Shinzo Abe's plans to revive Japan's economy, the world's third largest.
(Read more: Japan's GDP miss- What went wrong?)
Japan's economy grew 0.3 percent in the fourth quarter of last year from the previous quarter, below analysts' expectations for a 0.7 percent gain.
While Thursday's data showed weaker-than-expected growth in exports, they still marked an eleventh straight month of gains on the back of weakness in the yen and strong exports of cars.
The yen weakened more than 20 percent against the dollar last year and currency weakness has been a key element of Tokyo's plans to kick start the economy after years of lackluster growth and deflation.
"The GDP numbers were a bit of a surprise and we are expecting more easing from the Bank of Japan," said Martin Lakos, division director at Macquarie Private Wealth, speaking to CNBC after the Japan trade data.
Earlier this week, the Bank of Japan kept monetary policy steady and extended three special loan facilities by one year from their scheduled expiry at the end of March.
(Read more: BOJ stands pat on policy, extends special loans)
The move was seen by some analysts as "mini ease" to lend support to Japan's economy.
- Reuters contributed to this report