The latest data further illustrate the emerging impact of the March 11 disasters, in which a 9.0 magnitude earthquake and the tsunami it unleashed devastated swathes of the north east coast and triggered an atomic emergency.
Japan's trade surplus in March reached 196.5 billion yen ($2.37 billion), down 78.9 percent but still managing to stay in the black for the second straight month, the finance ministry said.
Exports in March fell 2.2 percent to 5.87 trillion yen, falling for the first time in 16 months due to reduced shipments of automobiles, it said.
The fall was led by vehicle exports, which contracted 27.8 percent, the ministry said, after Japan's leading automakers were forced to halt production amid broken supply chains and power shortages.
Imports rose for the 15th straight month, increasing 11.9 percent to 5.67 trillion yen, on surging prices of oil and iron ore, the ministry said.
The value of oil imports rose 14.8 percent. The value of iron ore imports soared 74.9 percent. Coal imports also rose 39.4 percent.
Procurement of manufacturing parts from overseas also boosted imports, analysts said.
The ministry also said Japanese exports for the year to March rose 14.9 percent to 67.8 trillion yen, while imports rose 15.9 percent to 62.4 trillion.
The annual trade surplus rose 3.9 percent to 5.4 trillion yen, the ministry said.