Putin visited a fish plant, a hospital and a school on Iturup, one of the chain's southernmost islands.
He also spoke briefly on Thursday to local residents and met the governor of Russia's Sakhalin region, Valery Limarenko.
Japan asserts territorial rights to the four southernmost islands of the chain, which it calls the Northern Territories.
The Soviet Union took them from Japan in the final days of World War II, and the dispute kept the countries from signing a peace treaty formally ending their hostilities.
Decades of diplomatic efforts to negotiate a settlement have not produced any visible results.
Moscow over the years has also beefed up its military presence on the Kuril Islands in moves that appeared to underscore its firm stance in the dispute.
Japanese Foreign Minister Toshimitsu Motegi said his country "strongly protests" against Putin's visit to Iturup, which Japan calls Etorofu.
"The Northern Territories, including Etorofu (Iturup) Island, are Japan's inherent territory both historically and from the perspective of international law," Motegi said in a statement.
Japan also protested in 2021 when Russia's Prime Minister Mikhail Mishustin visited Iturup.
Putin in recent days has visited several regions in Russia's Siberia and the Far East.
Before coming to Iturup, the Russian president stopped on Sakhalin Island to attend the final part of the drills by Russia's Pacific Fleet.
Speaking aboard a warship that was taking part in the naval exercises, Putin said Wednesday that the current status of the Kuril Islands "is enshrined in international documents as a reality that arose following the outcome of the World War II".
"But even here, Russia was prepared to seek a solution with the goal of concluding a peace treaty with Japan," he said.
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