The country's refineries remained in operation during the typhoon, the worst to hit Japan in decades, and there was no damage to facilities, refiners said.
Typhoon Hagibis made landfall on Japan's main island of Honshu on Saturday evening, leaving large areas of towns in central and eastern Japan under water. The death toll reached 66 on Tuesday and many homes remained without power or water.
JXTG Nippon, which is a unit of JXTG Holdings Inc, temporarily halted land shipments at the Negishi refinery due to flooding, but shipments had been restarted on Tuesday, a company spokeswoman said.
Refiners including Idemitsu Kosan, Cosmo Oil, a unit of Cosmo Energy Holdings, and Fuji Oil said sea shipments had been temporarily suspended as a precautionary measure, but all shipments had been resumed by Tuesday.
(Reporting by Yuka Obayashi; editing by Richard Pullin)