Prime Minister Shinzo Abe's government is to establish a task force to research owners and names of some 400 remote islands, the Yomiuri Shimbun said.
If their ownership is unclear, the government will give official names to the islands and nationalise them, the mass-circulation daily reported.
"(Japan) plans to end the research next year and quickly take action, including nationalisation, to remote islands with no ownership," the daily said.
The 400 islands are scattered across waters surrounding the Japanese archipelago.
The task force will comprise officials from the finance and justice ministries as well as the coastguard.
The move is part of Japan's efforts to preserve maritime resources as the country faces ongoing territorial disputes with its neighbours, the newspaper added.
In 2012, ahead of the planned project, Japan announced plans to give names to some 40 other islands, including some near those at the centre of a dispute with China, in an effort to verify the extent of the nation's exclusive economic zone.
Tensions have steadily risen between China and Japan, which accuses its powerful neighbour of sending an increasing number of ships to exert its claim over sparsely populated islands managed by Tokyo in the East China Sea.
The territorial row over the islands, known as Senkaku in Japanese and Diaoyu in Chinese, was reignited last September when Tokyo nationalised three islands in the chain in what it said was a mere administrative change of ownership.
Beijing has also disputed Tokyo's claim to Okinotorishima, which lies 1,700 kilometres (1,050 miles) south of Tokyo, saying the wave-swept atoll cannot be regarded as an island under the UN Convention on the Law of the Sea.