He said the aid was designed to encourage North Korea to continue its efforts to promote reunification with South Korea and to normalise relations with Japan and other democratic countries.
A government spokesman, Hidenao Nakagawa, said the move had been taken in response to an appeal from the United Nations World Food Programme.
He said the aid was designed to encourage North Korea to continue its efforts to promote reunification with South Korea and to normalise relations with Japan and other democratic countries.
"The purpose of the aid is to support the positive movement taking place in North Korea," Mr Nakagawa said.
Japan has no diplomatic ties with North Korea.
Millions threatened
North Korea is facing a sixth consecutive year of food shortages with aid agencies saying the on-going famine has already killed hundreds of thousands of people and continues to threaten millions.
A drought and two typhoons have worsened conditions in recent months.
The Japanese Government's announcement marks a five-fold increase in Tokyo's rice shipments to Pyongyang and will be the country's largest aid shipment to the North.
Tokyo suspended all aid in 1998 after North Korea test-fired a ballistic missile over Japanese territory, but it began lifting sanctions late last year.
Food loan
The latest aid package prompted a protest by a small group of relatives of Japanese citizens who were allegedly kidnapped by North Korean agents 20 years ago.
Last week South Korea also announced that it had agreed to provide 500,000 tons of food grain in the form of a long-term loan to North Korea.
Seoul said North Korea had promised that international observers would be allowed to monitor the distribution of food amid accusations that previous aid deliveries have been diverted to feed the country's military, one of the largest armies in the world.