He also called on both parties to peacefully resolve the long-running dispute.
Standing alongside Japanese prime minister Shinzo Abe, Mr Obama was speaking on the first full day of a four-nation visit to Asia.
In a show of solidarity with Mr Abe, the American President affirmed that a treaty between their countries would obligate the US to defend Tokyo in a potential clash with Beijing over islands in the East China Sea, called Senkaku by Japan and Diaoyu by China.
Mr Obama said the US takes no position on whether the islands are in the dominion of China or Japan, but he noted that Japan historically has administered the islands.
"We do not believe that they should be subject to change unilaterally," he said. At a news conference at the Akasaka Palace, Mr Obama said.
"What is a consistent part of the alliance is that the treaty covers all territories administered by Japan."