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Honda kept all its factories closed on Monday, except for a motorcycle plant on the southern island of Kyushu, though that too will be shut from Tuesday.
Meanwhile, the firm said in a statement that it would "fully cooperate" with rollover power outages planned by Tokyo Electric Power.
Honda manufactured 69,170 cars in January in Japan, where it makes 22 percent of its cars.
Its shares closed down 6.5 percent at 3,095 yen before the announcement, while the benchmark Nikkei 225 average sank 6.2 percent.
Shares of other Japanese automakers and manufactures also faced hefty selling as companies struggled to gather information from the stricken area and investors’ worried production could be suspended for an extended period.