Japanese restaurant chain Sukiya will temporarily shut nearly all of its roughly 2,000 branches after a rat was found in a miso soup and a bug was found in another meal, the company said on Saturday.

Sukiya, famous for its beef bowls, apologised in a statement saying a bug contamination at one of its Tokyo restaurants on Friday, two months after the rat incident at another branch.

"Sukiya has decided to temporarily close all restaurants, with the exception of some stores in shopping centres, from March 31 to April 4 in order to take measures against pests and vermin," it said.

The fast-food company has about 1,970 stores across Japan.

The Nikkei business daily reported that its stores in shopping centres will also be closed as soon as arrangements are made with the facilities.

Food recalls are rare in Japan, a country with famously high sanitation standards, but food poisoning and recall incidents occasionally make headlines.

Last year, more than 100,000 packets of sliced bread were recalled after parts of a rat were discovered inside two bags. (AFP)