The foreign ministry made the protest shortly after the plane entered Japanese airspace off the coast of the northernmost main island of Hokkaido, near a disputed island chain, yesterday afternoon.
"We made the protest through the Russian embassy in Tokyo," a foreign ministry official told AFP.
"The Russian side did not confirm the case, only saying they will check facts."
The Japanese Air Self-Defense Force scrambled four jets to head off the intruder, which it believed was Russian after analysing its course, a defence ministry official said.
Sixteen seconds after entering Japanese airspace, the plane left towards the Kuril island chain, claimed by Tokyo but controlled by Russia, the ministry added.
Soviet troops seized the islands, known as the Northern territory in Japan, just after Japan surrendered in World War II.
The seven-decade-old dispute has hampered trade and prevented Moscow and Tokyo from signing a formal post-war peace treaty.
A map on the defence ministry's website showed the plane crossed a halfway line between Japan's Nemuro peninsula and one of the four disputed islands, called Kunashir in Russia and Kunashiri in Japan.
Kishida's planned visit to Moscow was rescheduled in August after Tokyo hit out at Russian Prime Minister Dmitry Medvedev's trip to one of the disputed islands.
