Russia says President Medvedev plans more trips to a disputed group of islands also claimed by Japan.
Protests greeted the president’s visit to Kunashir, a remote island rich in fishing grounds and minerals.
In Moscow Japan’s ambassador was seen leaving the embassy after being recalled by Tokyo.
The Kremlin has not commented, but the foreign minister has reasserted Russia’s sovereignty.
Sergei Lavrov said: “This visit will allow the president to identify the tasks needed to resolve the region’s socio-economic problems. President Medvedev told me he will also visit the other islands.”
Although the dispute is embarrassing for Japan ahead of a major regional summit, foreign minister Seiji Maehara was straining to be positive at a news conference.
“We hope to clear up the questions regarding the ownership of the four northern islands and sign a peace treaty in order to establish even better relations between Japan and Russia,” he said.
Those relations are best described as stormy. Sovereignty has been disputed since Soviet troops moved in after World War II, but Medvedev is the first Russian leader to visit.
The row means Japan is at odds with both its biggest neighbours. It is also embroiled in another territorial dispute with China.