Kyodo news agency reported Education Minister Hakubun Shimomura said it is "natural for the state to teach properly about [Japanese] territory."
The move was guaranteed to be condemned by mainland China and South Korea, which also claim the territories in the East China Sea.
"With the cooperation of our Foreign Ministry, we will explain the country's position to our neighbors," Shimomura said.
The Senkakus -- called Diaoyu Islands by the Chinese -- cover 1,700 acres and lie 200 nautical miles southwest of the Japan's Okinawa island, and are 120 miles northeast of Taiwan and 200 miles east of the Chinese mainland.
Japan controls the Senkakus while South Korea has nominal control of the Takeshimas, maintaining a large lighthouse, helicopter pad and landing dock. Both territories are uninhabited.
Ownership of the Senkakus and the Takeshima islets increasingly is important because of surrounding fishing rights and the potential for exploiting any seabed oil and natural gas reserves.
"It is extremely important that the children who will bear our future can properly understand our territory," Shimomura said.
"We must make efforts to politely explain our position to both nations and seek their understanding."
Beijing and Seoul quickly condemned Japan's move to revise the teaching guidelines.
The 465-acre Takeshimas, formerly called Liancourt Rocks and known as Dokdo in Korea, are about 114 nautical miles from Japan's main island of Honshu and 120 nautical miles from mainland Korea.
South Korea's Yonhap news agency reported the foreign ministry in Seoul immediately demanded Japan withdraw the teaching guidelines.
A statement by the South Korean Foreign Ministry said Japan's "groundless claims" go against history, geography and international law.
"Our government strongly denounced it and demands an immediate withdrawal. If the Japanese government doesn't answer the demand, our government will sternly take actions against [the manuals]," the ministry said.
China's Xinhua news agency reported Beijing immediately "logged stern protest against the move and urged Japan stop provocative actions and respect historical realities."
Tensions rose further when China extended in November its air defense zone to include the Senkakus.
A country with an air defense zone -- which exists by unilateral declaration -- expects aircraft entering the area to identify themselves. Countries with such zones include Canada, India, Pakistan, Norway, the United Kingdom, Taiwan and the United States.
Japanese coast guard vessels constantly monitor Chinese fishing ships near the Senkaku islands and are wary of attempts by ships from any country to land.
Despite the war of words over ownership, Japan, Taiwan and China co-operated earlier this month to rescue a Chinese man after he failed to land his balloon on one of the Senkaku islands.
Kyodo reported the man, a 35-year-old cook from northern China's Hebei province, took off from China's southern coastal Fujian Province aiming to land on Uotsuri Island.
But bad weather and a mechanical problem forced him to ditch about 14 miles off the island.
The man radioed his problem to Taiwan's coast guard which relayed the message to a Japanese coast guard vessel.
Japanese coastal officials rescued him by helicopter and handed him over to a Chinese patrol ship.