In an interview ahead of his Asian tour, Mr Obama said the US would oppose any attempt to undermine Japan's control over the islands.
US officials have made such comments in the past, but this is the first time Mr Obama has given such explicit support.
He arrived in Japan on Wednesday ahead of stops in three other Asian nations.
China's foreign ministry has said it opposes the islands being covered by the defence treaty.
"The so-called US-Japan alliance is a bilateral arrangement from the Cold War and ought not to harm China's territorial sovereignty and reasonable rights," spokesman Qin Gang said in Beijing during a regular press briefing.
By Celia HattonBBC News, Beijing
Would China fight for disputed islands?
Mr Obama is not going to Beijing, but relations with China are expected to dominate his meetings with regional leaders.
The trip was an opportunity to reinforce the importance the US placed on Asia, former US Assistant Secretary of State PJ Crowley told the BBC.
"Many traditional allies... [also] value a strong US presence in the region to balance against an assertive China," he said.
The visit comes amid a "period of very significant tension among American allies, and between American allies and China", he added.
Mr Obama's trip - from 23-29 April - comes nearly seven months after he cancelled a visit to the region due to a government shutdown.
He will have a private dinner with Japanese Prime Minister Shinzo Abe, as well as bilateral meetings with the South Korean, Malaysian and Philippine leaders.
Ties between Tokyo and Beijing were expected to be high on the agenda as Mr Obama touched down in Tokyo on Wednesday evening.
Relations are severely strained over a raft of issues, including East China Sea islands - called Senkaku in Japan and Diaoyu in China - that both claim.
Japan controls the islands but Chinese ships have sailed repeatedly in and out of what Japan says are its territorial waters as Beijing presses its claim. Last year, China declared an air defence identification zone over the islands, drawing widespread criticism.
Ahead of his visit, Mr Obama said in a written response to Japan's Yomiuri newspaper that the US opposed "any unilateral attempts to undermine Japan's administration of these islands".
"The policy of the United States is clear - the Senkaku Islands are administered by Japan and therefore fall within the scope of Article 5 of the US-Japan Treaty of Mutual Co-operation and Security," he wrote.
Japan depends on the US for its security, under a decades-old alliance that dates back to the end of World War Two.
The US, however, is keen for Japan to take on greater responsibility for its own security - an area where Mr Obama and Mr Abe are likely to be in general agreement.
The two leaders are also expected to discuss the 12-nation Trans-Pacific Partnership (TPP), a trade deal which requires each country to strike an agreement with other prospective members.
A rift between Japan and the US over agriculture product tariffs has proved a major sticking point.
By Carrie GracieBBC China editor
Mr Obama is also expected to have to balance bolstering US ties with each Asian ally with improving communication among them, particularly between South Korea and Japan.
The two Asian nations are at odds over a separate set of disputed islands, as well as historical issues linked to Japan's war history.
The Japanese prime minister's views on World War Two have poisoned relations to the point where Tokyo and Seoul are now barely on speaking terms, reports the BBC's Rupert Wingfield-Hayes in Tokyo.
On Tuesday, Seoul accused Mr Abe of romanticising "Japanese colonialism and its war of aggression" after he sent an offering to the Yasukuni Shrine, where Japan's war dead - including convicted war criminals - are enshrined.
But the US - which last month brokered a meeting of the Japanese and South Korean leaders - wants the two to co-operate on North Korea, amid long-term deadlock in moves to end Pyongyang's nuclear ambitions.
On Tuesday, South Korea's defence ministry said that it had detected "a lot of activity" at the Punggye-ri nuclear test site.
North Korea could be planning to hold a "surprise nuclear test or just pretend to stage a nuclear test", a spokesman said.
Mr Obama arrives in Seoul on Friday. A state department spokeswoman said the US was "closely monitoring the situation". The test, if it went ahead, would be North Korea's fourth.
US President Barack Obama has assured Japan that islands at the centre of its territorial dispute with China are covered by a bilateral defence treaty.