The cyberweapon, a computer virus being developed by the Defense Ministry, has been undergoing tests in a closed network since 2008, the newspaper said.
Other countries, including the United States and China, are already said to be using cyberweapons.
Japan's Defense and Foreign ministries are working on legislation to govern use of cyberweapons, sources said.
The Defense Ministry's Technical Research and Development Institute, in charge of weapons development, outsourced to Fujitsu development of the cyberweapon virus as well as a system for monitoring and analyzing cyberattacks as part of a $2.27 million contract.
Fujitsu would not comment on the program, citing client confidentiality.
The cyberweapon can identify not only the source of the attack but other computers used to transmit a virus and to disable the attacking program while collecting relevant information.
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