The deficit for the month rose to 1.02tn yen ($10.5bn; £6.7bn), as imports surged 19.6% from a year ago.
The yen has fallen nearly 25% against the US dollar since November 2012, as policymakers unveiled a series of aggressive measures to revive growth.
Analysts said that despite the growing deficit, the government was likely to stick to its aggressive policies,
“In the short term the government will focus on its weaker yen policy as its priorities are very clear,” Junko Nishioka, chief Japan economist at RBS Securities in Tokyo, told the BBC.
“They want to revive growth in the Japanese economy and a weak yen is key to achieving that goal,” she added.