An unidentified Cabinet Information Research Office official is suspected of divulging information on Japanese foreign and domestic policies to a Russian Embassy official in Japan.
Police said the official at the Cabinet Secretariat's intelligence office had provided data on papers, frequently meeting with the Russian diplomat in 2007.
The Russian Embassy has yet to comment on the report. The Russian diplomat in question was reported to have left Japan some time ago.
Japanese Prime Minister Yasuo Fukuda, urged that tough measures be taken over the incident on Wednesday.
"It is deplorable that the incident took place right under my nose," Fukuda said. "A thorough investigation should be conducted and tough measures taken."
Echoing the premier's statement, Chief Cabinet Secretary Nobutaka Machimura said if the intelligence leak is confirmed, the official to blame should be subjected to "severe punishment."