Japan's foreign minister is in Russia for talks aimed at improving relations between the two countries.
Nobutaka Machimura's visit is meant to commemorate the first treaty signed by the two countries 150 years ago.
But it is overshadowed by a 60-year-old dispute over four islands known as the southern Kurils in Russia, and the Northern Territories in Japan.
Russia has said it may surrender two of the islands seized during World War II, but Japan wants all four returned.
On Thursday, Russian Deputy Foreign Minister Alexander Alexeyev said fundamental differences remained over the territorial dispute, which would not be quickly resolved.
"This work is ongoing and will continue. It is not easy and may require a lot of time," he was quoted as saying.
Mr Machimura's visit is also seen as paving the way for a visit by Russian President Vladimir Putin to Japan, tentatively scheduled for early this year.
It is hoped talks between the two leaders might lead to a breakthrough in the dispute, which has prevented the two sides from signing a peace treaty formally ending World War II hostilities.
Russia's Foreign Minister Sergei Lavrov suggested in November that Moscow might return two of the four islands seized by Soviet troops in 1945.
The offer is based on a promise by former Soviet leader Nikita Khrushchev, made in 1956, to return two of the islands - a pledge that was never fulfilled.
But Japanese Prime Minister Junichiro Koizumi said "Japan cannot be content" with the offer, insisting all the southern Kurils should be returned.
The islands and a cluster of outcrops are currently inhabited by a small community of Russian fishermen and their families.