Chief Cabinet Secretary Nobutaka Machimura made the statement after police accused a Cabinet Information Research Office official of divulging information on Japanese foreign and domestic policy to a Russian Embassy official in Tokyo, allegedly for a payment of 4 million yen ($36,000).
Machimura said the incident, denied by Moscow, had harmed Japan's prestige and the reputation of the Cabinet led by Liberal Democrat Yasuo Fukuda.
Police said the 52-year-old Japanese suspect confessed he had started contacting the Russians ten years ago. Two years ago, he met with the 38-year-old second secretary of the Russian Embassy, who he continued to meet regularly in bars and restaurants. "I transferred materials and received money," police quoted him as saying.
The Japanese official has been fired, the first dismissal from such a post since 1986. Police said they searched his house late last year and confiscated certain materials.
A source in the Russian Embassy who asked to remain anonymous confirmed to RIA Novosti on Thursday 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 embassy's press attache, Sergei Yasenev, called the police accounts confusing and regrettable, and said: "certain forces in Japan seem to be trying to cast a slur on Russia."