Although exports grew 11.5% in December, that was the smallest rise since the start of the year.
And shipments to top trading partner China slumped.
They were down over 6% on the year in value, and off by almost a quarter in volume.
The slowdown came as China was hit by renewed health-crisis concerns.
It's now uncertain how long the country will take to return to pre-crisis levels of demand.
Thursday's (January 19) data also highlighted the challenges for a country lacking in natural resources.
Japan's imports grew by over 20% in value terms, driven by soaring spending on oil, coal and gas.
That in turn is likely to stoke inflation, raising the cost of living and the price of doing business.
Put the numbers together and Japan was left with a trade deficit of over $11 billion in December.
That extends the run of deficits to 17 straight months.
For the year as a whole the shortfall hit almost $156 billion - the biggest figure since 1979.
