The announcement came after Russian President Vladimir Putin met in Moscow with visiting Japanese Prime Minister Shinzo Abe, RIA Novosti and RT reported.
"The heads of the two nations have expressed their resolution to overcome the existing differences in the parties' positions and to sign the peace treaty by finally solving the question in a mutually acceptable form," the two leaders said in a joint statement.
Abe said the decision to resume the negotiations that were put on the shelf in 2003 is a major development, though Putin cautioned there are sticky issues to unravel. The two countries never signed a permanent peace treaty at the end of World War II and also have rival claims to the Kuril Islands in the North Pacific.
"The negotiations have essentially been frozen in recent years and today we have agreed to resume contact in that area," Putin said.
"This does not mean that we will settle everything tomorrow, if the problem has not been resolved for the past 67-68 years. But at least we will continue to work on this complex issue that is so important for both countries."
Abe said the two countries agreed to set up a "2+2" negotiating format with their foreign and defense ministers meeting in an effort to enhance mutual trust "in the defense and security field."