The surplus came to 590.7 billion yen ($7.3 billion) in May, the finance ministry data showed, beating economists' median forecast of 300 billion yen.
The quake and tsunami, which struck the country's northeast on March 11, badly hampered factory production, sending exports plunging.
Japan's surplus in the current account -- the broadest measure of the country's trade with the rest of the world -- fell for the third consecutive month after the March disaster.
But with the supply chain rapidly coming back online, the latest drop in the surplus was smaller than a 69.5 percent plunge in April.
Japan logged a trade deficit of 772.7 billion yen in May against a year-before surplus of 402.7.
Exports fell 9.8 percent to 4.5 trillion yen, compared with growth of 34.0 percent a year earlier but better than a fall of 12.7 percent registered in April. Imports soared 14.7 percent to 5.3 trillion yen largely due to higher energy costs.
The current account measures trade in goods, services, tourism and investment.
Copyright APP (Associated Press of Pakistan), 2011
Copyright AFP (Agence France-Presse), 2011