Imports also rose from a year earlier for the first time in more than a year as the world's second-largest economy shook off the malaise of the global financial crisis.
The 40.9 percent annual jump in exports in January may be encouraging for the government, which has expressed concern that the rapid recovery in shipments to Asia may slow down.
January's jump in exports was the third-biggest on record, as shipments to China logged their biggest rise since August 1985 and those to the United States climbed for the first time in 29 months, finance ministry data showed.
Imports posted their first on-year rise in 15 months, due in part to higher oil and other raw materials prices. Imports rose 8.6% in January to 4.817 trillion yen.
Exports to Asia, which account for more than half of Japan's total exports, jumped 68.1 percent from a year earlier, faster than the 31.1 percent rise in the year to December.
Exports to China jumped 79.9 percent from a year earlier, while those to the United States rose an annual 24.2 percent.
Gains in Japan's exports to China were likely exaggerated as the Lunar New Year last year was in January, whereas this year the week-long holiday came in February, Shinke said. But he added that excluding this factor, exports to China were still healthy.
Japan's trade balance came to a surplus of 85.2 billion yen ($944.4 million).