Russia was hit with a wave of sanctions after it sent forces into Ukraine in February last year, but calls have grown from Kyiv and its allies for tougher action against Moscow.
The latest embargo by Tokyo follows the Group of Seven summit Japan hosted last week in Hiroshima, where the bloc's leaders agreed to "starve Russia of G7 technology, industrial equipment and services that support its war machine".
The new Japanese sanctions include "an asset freeze of Russian individuals and groups, a ban on the export of goods to Russia's military-related organisations, and a ban on the export of construction and engineering services to Russia," top government spokesman Hirokazu Matsuno told reporters.
The asset freeze targets 17 individuals and 78 groups, including high-level military officials, while the 80 organisations hit with export restrictions include the Russian mobile phone operator MegaFon, according to the Japanese government.
The United States, Britain and the European Union have all announced fresh punishments against Moscow recently, as well as commitments of more military aid to Ukraine, including F-16 fighters.
Matsuno also condemned plans to deploy Russian tactical nuclear weapons to Belarus.
Belarusian leader Alexander Lukashenko said Thursday that Moscow had begun moving nukes to its territory.
Matsuno said this will "further escalate the situation".
"As the only country to have suffered atomic bombings during wartime, Japan can never tolerate Russia's threat of nuclear weapons, not to mention their use," France 24 reports