The new measures include banning certain Russian banks from issuing securities in Japan and stepping up inspections to prevent arms being shipped to Russia, Chief Cabinet Secretary Yoshihide Suga said.
"We will continue to be in close contact with the other G7 nations and international society to seek a peaceful and diplomatic resolution to the situation in Ukraine," Suga told a news conference.
According to RIA Novosty news agency, the banks to be affected by the new sanctions include Sberbank, Gazprombank, Rosselkhozbank, VTB and Vneshekonombank.
Suga also said Japan had lodged a protest through diplomatic channels about the visit by Putin's chief of staff, Sergei Ivanov, on Wednesday to one of the contested islands, called the Northern Territories in Japan and Southern Kurils in Russia.
Russia's foreign ministry said on Wednesday it was disappointed with the new sanctions from Japan, calling them an "unfriendly step".
"We see this unfriendly step as fresh evidence of the inability of the Japanese side to enforce an independent foreign policy line," the statement said.
An aviation bomb was found and later neutralized in the Zverynas area of Vilnius on Thursday night.
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