The fast food company says it can't get hold of enough potatoes because of industrial action in America.
As a result they're having to ration French fries for customers.
"Unfortunately without this sales restriction step, we would run the danger of running out of fries at some of our stores around the end of the year," said McDonald's Japan spokeswoman Kokoro Toyama.
There are more than 3,100 McDonald's outlets in Japan.
For now they will only serve small portions of fries, though they won't restrict how many portions customers can order.
More than 1,000 tonnes of potatoes have already been flown in to try to boost supplies. They started arriving this week.
A further 1,600 tonnes will be imported by sea but they won't arrive until January.
The industrial dispute in America is between 20,000 dockworkers and terminal operators and shipping lines at 29 ports on the west coast of the United States.
This isn't the first time that Japan's been hit by a food shortage in recent weeks.
For most of this month supplies of butter have been so low that supermarkets have had to limit customers to one pack each.
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The company reported profits of $98m (£65m) for the quarter, after posting a big loss for the same period last year.
The Z10 handset is seen as crucial to the future of Blackberry, which has struggled to keep up with new Apple and Android phones.
It has been on sale for a month in the UK, Canada and other markets.
It went on sale with little fanfare a week ago in the United States, Blackberry's most important market.
The latest figures do not include US sales.
Blackberry was previously called Research In Motion, but changed its name last year.
Analysts greeted the results cautiously, saying that it was too early to judge the success of the Z10 and its sister device the Q10.
Earlier in the week, Blackberry shares were hit when two major US brokerages expressed disappointment with the US launch of the Z10.
In a note to its clients, Citigroup described the launch as "a big disappointment".
The Blackberry results also showed the company lost three million users over the year. Its handsets are now used by 76 million people, down from 79 million 12 months ago.
In total, Blackberry said it had shipped a total of about six million handsets in the three months to early March.
McDonald's in Japan is running out of chips.
[NEXT_CONCEPT]
Mobile phone maker Blackberry says it shipped one million of its new Z10 smartphones in the first three months of 2013.