Japan responded by scrambling eight fighter jets after the Chinese plane flew over islands at the centre of a long running dispute between the countries.
US Assistant Secretary of State for Asian and Pacific Affairs, Kurt Campbell, called for a peaceful resolution to the conflict.
"We are encouraging all sides to take appropriate steps so that there will be no misunderstandings, no miscalculations that could trigger an environment that would be antithetical to the maintenance of peace and stability," he said.
It was the first incursion by a Chinese state aircraft into Japanese airspace anywhere since Tokyo's military began monitoring in 1958.
The move marked a ramping-up of what observers suggest is a Chinese campaign to create a "new normal" - where its forces come and go as they please around islands Beijing calls the Diaoyus, but Tokyo controls as the Senkakus.
It also came as ceremonies mark the sensitive 75th anniversary of the start of the Nanjing Massacre, when Japanese Imperial Army troops embarked on an orgy of violence and killing in the then-Chinese capital.
F-15 jets were mobilised after a Chinese Maritime Surveillance twin turbo-prop aircraft ventured over the islands just after 11am (local time), chief cabinet secretary Osamu Fujimura told reporters.
"It was a fixed-wing Y-12 aeroplane belonging to the Chinese State Oceanic Administration. We confirmed that this aeroplane flew in our country's airspace," he said.
"It is extremely regrettable. We will continue to resolutely deal with any act violating our country's sovereignty, in accordance with domestic laws and regulations," he said, adding a senior Chinese diplomat had been summoned.
Japan mobilised eight F-15 jets and an E2C early-warning aircraft, the Asahi Shimbun reported, citing a defence ministry source. But the incident appeared to have passed off without any direct confrontation.
In Beijing, China's foreign ministry said the flight had been routine.
"China's maritime surveillance plane flying over the Diaoyu islands is completely normal," said spokesman Hong Lei.
"China requires the Japanese side to stop illegal activities in the waters and airspace of the Diaoyu islands," Mr Hong said, adding they were "China's inherent territory since ancient times".
The incident came as Japan's coastguard chief told reporters he was digging in for a protracted dispute.
"As China has publicly said it will make this a permanent situation, we are preparing to be better equipped for this long, drawn-out contest," Takashi Kitamura, the commandant of Japan Coast Guard, told a news conference.
"Because we have various other responsibilities other than patrolling for border security, we are asking government to consider building up our capacity," he said.
Chinese government ships have moved in and out of waters around the islands for more than two months - four vessels were there for several hours on Thursday.
Such confrontations have become commonplace since Japan nationalised the East China Sea islands in September, a move it insisted amounted to nothing more than a change of ownership of what was already Japanese territory.
But Beijing reacted with fury, with observers saying the riots that erupted across China had at least tacit backing from the Communist Party government.