The White House said in a statement on Thursday night that Obama had scrapped travel to Bali and a subsequent trip to nearby Brunei for the East Asia Summit.
"Due to the government shutdown, President Obama's travel to Indonesia and Brunei has been cancelled," the White House said. "The President made this decision based on the difficulty in moving forward with foreign travel in the face of a shutdown, and his determination to continue pressing his case that Republicans should immediately allow a vote to reopen the government."
He will miss two summits, including the Asia-Pacific Economic Co-operation (Apec) meeting in Indonesia.
The White House said Obama had phoned Susilo Bambang Yudhoyono, president of Indonesia, on Thursday night to tell him he could not attend.
"He expressed his regret that the ongoing government shutdown in the United States will prevent him from attending the summit," the statement read.
The White House added that Obama "reaffirmed the close partnership that he has forged with Malaysia and respect for Prime Minister Najib's leadership, and committed to travel to Malaysia later in his term" and "welcomed Malaysia's strong leadership of the Global Entrepreneurship Summit".
Secretary of State John Kerry will take President Obama's place in Bali.
Mr Obama cancelled visits to Malaysia and the Philippines earlier this week because of his budget struggle with Republicans in Congress.
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