The weapon is the culmination of a 179 million yen ($2.3 million) three-year project entrusted by the government to technology maker Fujitsu Ltd to develop a virus and equipment to monitor and analyse attacks, the daily said.
The United States and China are reported to have put so-called cyber weapons into practical use, Yomiuri said.
Japan will have to make legal amendments to use a cyber weapon as it could violate the country's law against the manufacture of a computer virus, the daily said.
In November a computer system run by about 200 Japanese local governments was struck.
In October, Japan's parliament came under cyber attack, apparently from the same emails linked to a China-based server that have already hit several lawmakers' computers.
It was also reported that Japanese computers at embassies and consulates in nine countries were infected with viruses in the summer.
Currently, the virus is being tested in a "closed environment" to examine its applicable patterns.
