The firm said it would lose a worse-than-expected 21.8 billion yen (USD 186 million) for 2014 -- reversing a year-earlier profit -- as sales plunged in the wake of the embarrassing discoveries.
The unit's Canadian chief Sarah Casanova said the poor results marked a "harsh evaluation" by wary customers when she appeared at a press conference in Tokyo. She bowed deeply in an act of contrition common for executives in Japan.
A human tooth was found in some french fries sold at an Osaka outlet last year, the firm admitted in January.
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.
Two days later, a Japanese woman claimed to have discovered what was later identified as "dental material" in a McDonald's hamburger from northernmost Hokkaido in September.
Japanese media reported several other cases of contamination, including a piece of metal in a pancake.
The firm gave no estimate for earnings this year.
"When we received claims from customers we took each of them seriously," Casanova said.
"Regrettably, we were not able to always identify the cause of the issue...We will have to work harder than ever to regain the confidence of our customers. We'll do whatever it takes."
McDonald's has been operating in Japan since 1971.
Japan generally has a good record on food safety, and its consumers are used to high standards.
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