Giants of the fast food and "family restaurant" sectors, which serve Western style meals with a Japanese twist, are dependent on imports, Kyodo News reported, citing the chains and the Japan External Trade Organization.
But a dockworkers' dispute on the US West Coast has caused a months-long slowdown, creating a backlog and crimping imports to Japan.
The Japanese arm of McDonald's has been having problems since mid-November, Kyodo said, while Royal Holdings, which runs several family restaurant chains, said it has a few months' worth of stock, but was keeping a close eye on things.
News of the chip woes came with Japan already in the throes of a butter shortage that is threatening to ruin Christmas for millions of cake-baking Japanese housewives.
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Supermarket shelves have been empty for weeks, with any new stock disappearing almost as fast as it arrives, despite store-imposed limits of one pack per customer.
However, there was a glimmer of hope yesterday, with the farm ministry announcing four of Japan's major butter producers would up their output by a third to meet demand.
The ministry earlier said a sweltering summer had left the nation's cows exhausted, and sapped their milk-producing ability.