Russia, which is holding manoeuvres around the disputed Kuril islands, denied any such intrusion.
Former Japanese PM Yoshiro Mori is due to visit Moscow later this month to discuss territorial matters.
Yesterday was Japan's Northern Territories Day, when rallies are traditionally held calling for the return of the disputed islands.
Prime minister Shinzo Abe told a rally he would press ahead with negotiations for the return of the islands.
"I had telephone talks with President Putin in December, and told him I would like to find a mutually acceptable solution," Mr Abe said.