"We believe there will be some impact on revenue," said Kenji Kaniya, a spokesperson for Japan's version of the US burger chain.
"However, while there may be some people who won't come to our shops because of the lack of chicken nuggets, others may not feel that way and will buy our other products."
McDonald's began halting sales of chicken nuggets from March 22 as stocks ran out, with more than 90% of over 3 800 Japanese outlets ceasing nugget sales by Wednesday.
The firm expects to restart selling nuggets by mid-April after shifting its imports so they come mainly from certain regions in China and Thailand - countries not included in a partial ban on US fowl.
The Japanese agriculture ministry prohibited all chicken from the United States after flu was discovered in fowl from Pennsylvania in January, a spokesperson said.
But after recent reassurances, the ban now applies only to chicken from the states of Pennsylvania, Maine and Virginia.
Japan has forbidden chicken imports from certain regions of China since last June following the discovery of the Newcastle virus, and an all-out ban on Chinese duck, goose and quail also remains in effect.
McDonald's bottom line has already been hit this past year after the discovery of three cases of mad cow disease, a brain-wasting illness found in cattle, in Japan that has sent beef prices plummeting.
In the year to March 2001, net profit at McDonald's plunged 39.4% from 2000 to ¥10.2 billion, with pre-tax profit down 35.4% at ¥18.9 billion. Annual sales inched up 1.1% to ¥361.67 billion. - Sapa-AFP