A customer complained to the Japanese arm of the fast food giant after finding a foreign body in a serving of potatoes from an outlet in Osaka, two senior vice presidents told a press conference in Tokyo.
An independent investigation ordered by McDonald's determined that the object was a tooth but concluded that it had not been cooked, said McDonald's Japan senior vice president Hidehito Hishinuma.
"We were not able to discover how it got in the food," he said.
The customer, a mother with a small child, told a TV station that the store manager who visited her said the tooth had been "fried".
"I received an apology only when the store manager came over," the customer, whose name was not revealed, told the JNN network.
"The manager didn't really talk about how it got in and what action they will take in the future.
"I have a small child and it terrifies me to think that they could have eaten it and choked," she said.
McDonald's said there were no employees missing a tooth at the outlet and it believed there was a very low possibility of contamination at the US factory that had shipped the chips.
The incident is the latest public relations setback for the firm, and comes after a customer found a piece of vinyl inside a chicken nugget at an outlet in the northern city of Misawa. There was a similar case of contamination at a Tokyo branch.
The company also said a tiny piece of hard plastic was found in a sundae in the northeastern city of Koriyama in December.
Executives confirmed during the press conference that a small child who chewed on the plastic suffered a cut inside the mouth.
"We express our deep apologies for the worries and nuisance caused to customers by the foreign items found in food," McDonald's Holdings Japan senior vice president Takehiko Aoki told reporters.
The president of McDonald's Japan, Sarah Casanova, did not appear at the press conference. The company said she was abroad on a business trip, but was heading back to Japan in the wake of the incidents.
The discovery of bits of plastic and a tooth in menu items comes as McDonald's struggles to recover from the reputational battering it took in the summer when a Chinese supplier was found to be mixing out-of-date meat with fresh produce.
In July, Chinese officials shut Shanghai Husi Food Co after a television investigation revealed the dodgy practice. McDonald's switched to a Thai producer.
Late last year the company had to airlift an emergency supply of french fries from the US after a chip shortage had resulted in rationing at its 3,000 restaurants across Japan.
Labour disputes on the US West Coast had bunged up the export chain, leaving Japanese firms scrambling to secure fresh supplies.
The difficulties looked set to hit McDonald's bottom line.
In October, McDonald's Japan said it was on track to report a $143 million annual loss for 2014.
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The reputation of McDonald's in Japan and other countries is at stake, but different stories will keep on emerging from different quarters.
In Pakistan, the quality of McDonald's has also gone down from bad to worst as per its international standards.
Thanks to people of Pakistan that they don't want to share their views and experiences with ET.
By the way my family and I have not gone to McDonald's for more than a decade as we all know very well that McDonald's is a junk food and we don't want that our bodies should go out of shape.