Mr Ota only took over his portfolio in August this year
Japan's farm minister, Seiichi Ota, has tendered his resignation because of a food scandal involving tainted rice.
Mr Ota's ministry has admitted it was told in January 2007 that a food company was distributing rice tainted with pesticide.
Mr Ota had earlier said he saw no need to make "too much of a fuss over it".
It has since emerged that the rice, destined for industrial uses, was resold as a food product and served to the elderly.
The rice has been found to be tainted with pesticides and mould, and was known to be unfit for human consumption.
No-one has been reported as ill as a result of eating the rice; a government official said this was because the density of contaminants was low.
"I met Prime Minister [Yasuo] Fukuda and told him my decision to resign, considering the seriousness of the tainted rice problem for the society," Mr Ota said.
Japanese broadcaster NHK said his resignation had been accepted.
Japan faces general elections soon, possibly as early as next month.
As information trickled out, it became clear that the bad rice was sold to more than 300 firms, including brewers, food ingredient wholesalers and sweet makers.
A government report released this week showed that the rice was imported from China, Vietnam and elsewhere, and intended for use in the making of glue and other industrial products.
Instead, the Osaka-based Mikasa Foods company sold the rice on to firms which used it for making foods that have been distributed to hospitals and care homes.
Young people have also been affected as the bad rice was used in making some snacks sold in convenience stores, and in school lunches.
Japanese media reported that police said on Wednesday that the president of one of the small companies that had bought the rice from Mikasa Foods, had committed suicide by hanging himself.
When Mr Ota's ministry first heard of the tainted rice entering the food chain, he said it was unable to uncover any wrongdoing.
Mr Ota only took over the portfolio in August this year.
The BBC's Chris Hogg in Tokyo says the minister has come under fire after admitting his ministry "overlooked" the illegal distribution of rice unfit for human consumption.
Our correspondent says Mr Ota is known for his slips of the tongue, such as his expressed confidence that no-one would die from eating tainted rice and that no fuss was necessary.
The senior bureaucrat at the agriculture ministry had already resigned.