"The agency has information that during 2000-2001 the cruise missiles were illegally exported from Ukraine to Iran and China," a defense agency spokeswoman said.
The missiles, developed in the former Soviet Union, are capable of carrying nuclear warheads, according to the Sankei Shimbun newspaper.
The daily said Sunday that those missiles might have been sold to North Korea, a military threat to neighbouring Japan.
"As Japan considers the move significantly destabilizing for regional security, we have asked the Ukrainian government for a full investigation into the incident and preventive measures," the agency spokeswoman said.
"Japan does not have information as to whether the technology for the cruise missiles has been spread to North Korea," she said.
The international community is trying to bring Pyongyang back to the negotiating table in a bid to stop the Stalinist state's nuclear weapons programme. It says it already has nuclear arms.
Iran insists its nuclear programme is only to generate electricity. But hardliner Mahmood Ahmadinejad's victory in the country's presidential election has fuelled fears Tehran may revive its nuclear ambitions.
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