"We should have a more balanced food supply in the world," Eiichi Hayashizaki, a rice farmer at the protest, said.
"Japan imports the majority of its food from overseas, so we don't starve ourselves, but the government should stop controlling rice production in the country," he said.
Oxfam International has said that soaring food prices and climate change are having a negative impact on world poverty.
"This isn't the time for a holiday, this is the time for sorting out problems," Lucy Brinicombe, an Oxfam International spokesperson, said.
"They shouldn't be distracted from finding solutions for the food crisis and climate change."
Earlier this week, Robert Zoellick, president of the World Bank, called for G8 leaders to address rising food prices at their summit.
The crisis, which is limiting many poor peoples' access to staple foodstuffs, is a "man-made catastrophe" which is overwhelming the bank's resources, he said.
Global food prices have nearly doubled in three years, according to the World Bank.
There have been a string of protests in parts of the developing world over the sharp price increases.
Leaders of the eight major industrial powers - Britain, Canada, France, Germany, Italy, Japan, Russia and the United States - are reportedly set to install a system of "food reserves" to help nations that have limited immediate access to food.
Activists said that Japanese immigration authorities barred the entry of more than two dozen South Koreans who planned to take part in Saturday's demonstration.
South Koreans have a reputation for being particularly impassioned on issues of global trade.
A farmer from South Korea stabbed himself to death in 2003 during a protest at global trade negotiations in Mexico.