The disappointing figures, while expected, come after the deficit has steadily declined since the huge USD 1.4 trillion deficit Obama inherited after the deep 2007-2009 recession and the associated fiscal crisis.
According to many economists, the improving economy, tax increases on higher-income earners and cuts to annual agency budgets have helped close the gap but the longer-term picture is troubling.
"Over the last seven years, the administration and the American people have worked to rebuild our economy and ensure that it is the strongest, most durable economy in the world," the director of the Office of Management and Budget, Shaun Donovan, said in a blog post accompanying the report.
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Neither Democrat Hillary Clinton nor Donald Trump has focused much on deficits and debt in their presidential campaigns, but the rising figures may lend more urgency to the issue.
Trump has promised huge tax cuts that analysts say would pour trillions of dollars of debt onto the government's books. Clinton has promised tax increases on the wealthy but would turn around and spend the money on infrastructure, subsidizing college education and other initiatives.
The administration's forecast that the economy, as measured by the gross domestic product, will grow by just 2.2 per cent this year is still more optimistic than many other forecasters.