The statement has been criticized at a time when the pressure on the government is increasing ahead of the election in July due to rising food prices - including twice as expensive rice in the past year.
In a time when people are struggling with high rice prices, I made an extremely inappropriate comment, says Eto on Wednesday.
With the critical timing of the issue of rice prices, I have drawn the conclusion that it is no longer suitable for me to remain, he continues.
Eto has played a key role in ongoing trade negotiations with the USA. Increased import of rice from the USA has been mentioned as a possible concession that Tokyo can offer Donald Trump in exchange for lower tariffs.
Eto said over the weekend that he had never had to buy rice on his own, since his supporters had given him so much.
He is the first minister to resign in the minority government since Prime Minister Shigeru Ishiba took office in October.
