Kan previously expressed his "disappointment" over Medvedev's visit to one of four islands Japan claims control of, RIA Novosti reported Saturday.
Medvedev is in Japan for the Asia Pacific Economic Cooperation summit this weekend.
"Just as Kan expressed disappointment over ... (Medvedev's) visit to Kunashir Island, our assessment of the situation is that the president decides himself which region of Russia he visits," Russian Foreign Minister Sergei Lavrov said. "This is and will remain our territory."
Medvedev inflamed a long-standing dispute between the two countries when he visited the island earlier this month. Both countries have claimed the islands since they were occupied by the former Soviet Union at the end of World War II, the report said.
The dispute has prevented the countries from signing a peace treaty to formally end the war.