Japan has said it is lodging a strong protest with North Korea over what Tokyo sees as its lack of co-operation over missing Japanese nationals.
Megumi Yokota's parents believe she is still alive
Pyongyang has admitted kidnapping some Japanese to train its spies, but denies any are still alive in the country.
But Japan is sceptical and said on Friday that the evidence it had so far received was unsatisfactory.
Analysts say the protest could signal a move to impose sanctions on Pyongyang, which would seriously inflame tensions.
Chief cabinet secretary Hiroyuki Hosoda told reporters on Friday that Tokyo had rejected North Korean evidence, which was supposed to prove that two kidnap victims were dead.
This evidence was in the form of human remains handed to a Japanese delegation in November on a fact-finding mission about the kidnap victims.
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
Pyongyang said the remains were of Megumi Yokota, whom North Korea admits kidnapping in 1977 when she was just 13, is alleged to have committed suicide in 1994.
But Japan said earlier this month that DNA tests proved the remains in fact belonged to several other people.
Mr Hosoda said a letter of protest was being sent to Pyongyang via Beijing, and that Tokyo was demanding another investigation as soon as possible.
"The government will continue to seek a quick, sincere response from North Korea," he said.
"But if there's no response... Japan thinks it has no other choice than to take a severe stance," he said, without elaborating.
Tokyo has already suspended food aid to Pyongyang after determining the results of the DNA tests, and is under strong public pressure to impose economic sanctions to the North.
Japanese Prime Minister Junichiro Koizumi said on Friday that he wanted to leave "all kinds of options open".
He has previously indicated that sanctions - which could involve restricting Japanese port calls by North Korean vessels, remittances from Koreans living in Japan to the North, and imports of North Korean foods such as sea food and specialist mushrooms - would be a last resort.
North Korea has warned that sanctions would be tantamount to a "declaration of war".
Pyongyang insists the remains it has given Japan are genuine, and said on Thursday that Megumi Yokota's alleged North Korean husband has asked for them back.
Pyongyang admitted in 2002 to abducting 13 Japanese nationals, who were to be used as cultural trainers for North Korean spies.
Five were allowed to return to Japan, while North Korea said the others had died.