Some Japanese are left struggling to buy rice, the nation's beloved staple food, as the threat of a "megaquake," coupled with a series of typhoons and a week-long holiday, impacted the supply.

With daily stocks running out at some stores, the government warned against panic buying on Tuesday.

"We could only procure half the usual amount of rice this summer and bags of rice get quickly sold out," a clerk at a branch of the popular Fresco supermarket chain told Agence France-Presse (AFP) in the Japanese capital.

Rice shelves in some stores were emptied, and stocks were rationed after a government warning this month – since lifted – of a possible "megaquake," as well as several typhoons and the annual Obon holiday.

Other factors include lower harvests caused by hot weather and water shortages and increased demand related to record numbers of foreign tourists.

At one food store in Tokyo, a sign seen by AFP read: "For many customers to be able to buy, we ask you to purchase one (bag of rice) a day per family."

'No prospects'

A worker at another store in Tokyo said: "We can't purchase any rice at all, and there's no prospect of buying anytime soon."

The Fresco worker told AFP that daily stocks ran out by midday.

"Customers queue up before the store opens, but piles of bags, each containing 10 kilograms (22 pounds), are always sold out during the morning," he said.

Farm minister Tetsushi Sakamoto appealed for calm Tuesday.

"Please be cool-headed in your purchase activity by buying only the amount of rice you need," Sakamoto said, stressing, "The supply shortage situation will be gradually resolved.

Rice is deeply ingrained in Japanese culture, and its harvesting has shaped the nation's landscape, even though it was used as a currency in the seventh century.

With an annual consumption of seven million tons per year, it is by far the most consumed food staple in the country.

Demand has been falling for some time, however, because of a declining population and changing eating habits by many Japanese as they opt for alternatives.

The nation's stockpile in June was the lowest since 1999 when comparable data was first collected, but officials believe the inventory is sufficient.

A new harvesting season has started, with 40% of the crop available by the end of September, a farm ministry official told AFP.