Tokyo-Moscow relations are hamstrung by a row dating back to the end of World War II when Soviet troops seized the southernmost islands in the Pacific Kuril chain, known as the Northern Territories in Japan.
The tensions have prevented the countries from signing a peace treaty formally ending wartime hostilities, hindering trade and investment ties.
Russian Foreign Minister Sergei Lavrov told reporters that the leaders had discussed the disputed islands at talks that had focused on boosting trade ties but remained vague on the prospects of solving the conflict.
Abe's visit to Russia - his second this year - comes days after the Kremlin announced that Putin will travel to Japan in December, his first trip there since 2005.
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Putin said in an interview with Bloomberg News ahead of the talks that Moscow was seeking a "solution where neither party will feel... Defeated or a loser."
"We are not talking about some kind of exchange or some kind of sale," he said.
Over the years, leaders from the two nations have tried to make progress on resolving the row but a solution has proved elusive.
The two sides, meeting on the sidelines of an economic forum in the far eastern city of Vladivostok, had expressed the hope of easing some of the tensions surrounding the contested islands.
"I'm resolved to make progress on the peace treaty and territorial issues by holding candid and thorough talks with President Putin," Abe told reporters before he set off for Vladivostok.
"Japan is not ready to drop its claims to the islands and Russia will by no means recognise them," Russian political analyst Konstantin Kalachev said.