The proposal means that resolving the bilateral issue on the northern territories would effectively be put aside and a conclusion of the peace treaty would happen first.
He made the remarks while meeting Japanese Prime Minister Shinzo Abe at the Eastern Economic Forum in Russian Federation.
Later in the same session, Putin said of his offer: "I was not joking".
Seventy-three years after the war concluded, the two countries remain technically at war because of a territorial dispute over four Pacific islands.
Russian strongman Vladimir Putin and China's Xi Jinping buttered each other up Tuesday - tossing pancakes on the sidelines of an economic forum. So far, this diplomatic roadblock has stopped the two countries from signing a peace accord.
Xi and Putin had their third meeting in four months, charting the future course of the China-Russia comprehensive strategic partnership of coordination and exchanging views on major global and regional issues, Wang said. "Putin does not expect anything", Kunadze told Echo of Moscow radio station.
A former Russian deputy foreign minister, Georgy Kunadze, said he doubted that Putin wanted to solve the territorial problem in earnest.
Abe praised his meeting with Xi, saying they held "highly significant talks regarding Japan-China relations and the various issues that we face together".
Russian President Vladimir Putin on Wednesday said North Korea must be given security guarantees in exchange for steps towards denuclearization.
A Japanese government spokesman said the country's stance had not changed.
The strategic guidance by and close contact between the heads of state of China and Russian Federation serve as powerful engines for the development of bilateral relations, Wang said.
The Japanese prime minister said the two countries "have a duty to future generations".
The Kurils, which lie north of Japan's Hokkaido island, have been controlled by Moscow since they were seized by Soviet troops in the dying days of World War II. "We have been negotiating for 70 years", Putin said.
His comments came just days after confessing that the territorial dispute between Japan and Russian Federation, which has dragged on for decades, was unlikely to be resolved in the near future.