Japan approved sanctions against Iran last month, but US officials have been urging Tokyo to adopt tougher measures.
Many states fear Iran's nuclear programme is developing atomic weapons; Iran insists its programme is peaceful.
Japan is a major importer of Iranian crude oil, but it did not impose any restrictions on oil imports from Iran.
"We took these steps as they are necessary to push for nuclear non-proliferation and prevent its nuclear development," Chief Cabinet Secretary Yoshito Sengoku told a news conference.
"We have traditionally close relations with Iran and from that standpoint, we will patiently encourage the country towards a peaceful and diplomatic solution," he added.
The United States, the European Union, Canada and Australia have also announced additional sanctions, which have been opposed by Russia and China.
China is now Iran's closest trading partner, and has major energy interests in the country.
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