Police suspect an official at the Japanese Cabinet Information Research Office of handing over classified information to a Russian Embassy staffer, an allegation that the embassy has dismissed as an attempt by "certain forces" to harm bilateral relations.
A RIA Novosti correspondent in Tokyo reported that nationalists drove through a central area of the city in black buses equipped with PA systems, blaring out the slogans: "Clean the country of Russians!", "Go back to Russia!", and "give back our sovereign territory!", the latter being a reference to the disputed South Kuril Islands annexed by the Soviet Union after WWII.
Additional police have been deployed at the site of the protests, and Russians working in the area, in which the Russian trade representation and a RIA Novosti office are based, have been told to take extra care when on the streets.
The far-right activists are known to be fierce opponents of Prime Minister Yasuo Fukuda's Liberal Democratic Party, and have called for a re-establishment of the pre-WWII imperial cult in the country, when the emperor was considered a deity.
Visits of Russian officials to Tokyo are often accompanied by similar protests, albeit on a smaller scale.
Premier Fukuda on Wednesday said the alleged spying incident was "highly regrettable," and called for "tough measures."
A source in the Russian Embassy who asked to remain anonymous confirmed to RIA Novosti that during 2007 an embassy staffer, who has now left Japan, met on several occasions with an official of Japan's Cabinet Information Research Office.
The role of the office is to gather and analyze information for the prime minister and Cabinet members. The service's work includes processing data received from spy satellites.
Japanese police say the documents allegedly passed over did not relate to national defense, but to information on public developments in the country and confidential recommendations from the intelligence office to the government.
The 52-year-old Japanese official accused in the case faces imprisonment for divulging state secrets.
On Wednesday, the head of the Russian Embassy's consular department, Oleg Ryabov, was summoned to the Japanese Foreign Ministry. The diplomat was told that if the spying allegations are confirmed, "this will prove to be a highly serious incident."
Russia's Foreign Ministry has called on the embassy to fully cooperate with Japanese authorities on the issue.
The latest spying scandal is not the first to break out between the two countries. Moscow was last accused of obtaining confidential military information in Tokyo in 2000, and before that in 1980.
A key stumbling block in relations between Russia and Japan has been the contested ownership of the South Kuril Islands. The dispute, simmering for over 60 years, has kept the two countries from signing a formal peace treaty following World War II.
The countries have been involved in frequent disputes over Japanese vessels' poaching in Russia's Pacific waters. In August 2006, a Japanese fisherman was shot dead near the Kuril Islands when Russian border guards opened fire at his boat after it refused to stop.
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