The move comes after the United Nations last month added Ocean Maritime Management to a blacklist of North Korean companies that have violated a UN embargo on shipping weapons to the isolated communist state.
A year ago, the North Korean freighter was seized by the Panamanian government which discovered it was carrying Cuban military hardware, including Soviet-era arms.
A Japanese foreign ministry official did not have details on assets held by the firm in Japan, but he said the new measures would also monitor its financial transactions in the country.
The ministry official said the asset freeze was not likely to affect those talks.
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"This measure is basically separate from the bilateral talks and we don't think it will have any impact on them," he told AFP.
North Korea admitted in 2002 that it had kidnapped 13 Japanese citizens in the 1970s and 1980s to train its spies in Japanese language and customs.
Five of the abductees returned home but Pyongyang said -- without producing credible evidence -- that the eight others had died.
Pyongyang's vow to probe all unsettled cases has prompted Tokyo to ease some of its separate sanctions -- which are in addition to international penalties imposed after UN Security Council resolutions in the wake of nuclear and missile tests carried out by the North.