The row is over Japanese nationals missing in North Korea
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Japan has frozen food aid to North Korea in protest at Pyongyang's failure to co-operate in a probe into Japanese citizens kidnapped by the North.
Japan was outraged last week when DNA tests showed that remains provided by the North were not those of a missing Japanese woman, as Pyongyang claimed.
Japan promised impoverished North Korea 250,000 tonnes of food aid last May, but has so far only sent half.
Japan has yet to decide if it will take further measures, such as sanctions.
Japanese Foreign Ministry press secretary Hatsuhisa Takashima told BBC News that North Korea's behaviour meant Tokyo would not send it any more food aid for now.
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JAPAN'S MISSING
Snatched in the '70s and '80s
Used as cultural trainers for N Korean spies
Five allowed home in 2002
Five children now freed from N Korea
Eight said to be dead, others missing
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"Because of North Korea's unfaithful attitude, we thought it is not appropriate for us at the moment to have the remaining half distributed," he said.
The move follows the revelation last week that bones provided by North Korea to prove that a missing Japanese national, Megumi Yokota, was dead, transpired not to belong to her, but to several other people.
"It was a kind of unthinkable situation for us and the Japanese public is furious about that," Mr Takashima said.
Japan's Prime Minister Junichiro Koizumi said on Monday that he could understand the public anger against North Korea, but that it was too early to respond to growing calls for sanctions.
Possible measures include stopping North Korean ships visiting Japan, and preventing cash remittances from Japan to the North.
Pyongyang has admitted kidnapping Megumi Yokota in 1977, but said she committed suicide in 1994.
But Japan has remained sceptical, and had called for proof that she was dead.
The remains were brought back by a Japanese delegation last month after a fact-finding mission about kidnap victims who have gone missing in the North.
Pyongyang admitted in 2002 to abducting 13 Japanese nationals in the 1970s and 80s, who were to be used as cultural trainers for North Korean spies.
Five were allowed to return to Japan in 2002, while North Korea said the others had died or never entered the country.