The trade balance came in with a $7.3 billion gap, as exports dropped 16.4 percent and imports fell far less, dropping 4.1 percent.
Neither exports nor imports had fallen in the past seven years, Kyodo news agency reported Thursday.
Vehicle exports to Europe and the United States declined, as did the export of electronics equipment to other Asian countries. Imports of coal and liquefied natural gas grew, while imports of crude oil dropped 0.4 percent in the year that included average oil prices of $92.60 per barrel.
"The Japanese people, lawmakers and government must take the results seriously," Finance Minister Kaoru Yosano said.
During the year, Japan's surplus with the United States dropped 43 percent, with exports falling 27.2 percent and imports dropping 11.5 percent.
Japan's surplus in trades to Europe also dropped, falling 39.7 percent on a 23 percent drop in exports and a 12.3 percent drop in imports.