Exports by Japan fell 45.6% in March from a year ago due to a slump in overseas demand.
The finance ministry said on Wednesday the trade surplus plunged 99% last month from a year earlier to 10.96 billion yen ($US111 million).
For the 12 months through March, Japan recorded a trade deficit of 725.3 billion yen - its first shortfall for a fiscal year since 1980.
The economy recorded its worst performance in almost 35 years in the last quarter of 2008, contracting at an annualised pace of 12.1%.
The downturn has inflicted heavy losses on companies such as Toyota and Sony, prompting a wave of job cuts.
