It was the fourth straight year the annual deficit exceeded $1 trillion.
Geithner and Jeffrey Zientz, a deputy director of the Office of Management and Budget, said the FY 2012 deficit was $238 billion less than forecast in the budget President Barack Obama proposed in February.
Geithner said in a news release the Budget Control Act of 2011 was "a significant down payment on deficit reduction" because it cut almost $1 trillion in discretionary spending during a 10-year period. Geithner said the cuts reduced discretionary spending "to the lowest level as a share of the gross domestic product since at least the Eisenhower administration."
He called on Congress to take action on steps Obama has proposed to "enact a balanced deficit reduction package, including both spending and revenue components, along the lines of the $4 trillion deficit reduction proposals he offered in his February budget and in his submission to the Joint Select Committee on Deficit Reduction in September of 2011."
The report issued Friday said the 2012 deficit of $1.089 trillion amounted to 7 percent of GDP, down from 8.7 percent in FY 2011. The decline was attributed to a combination of higher revenues and a $61 billion reduction in outlays from 2011.
"The increased receipts can be attributed to the expiration of certain tax provisions and a stronger economy," the report said.
Corporate income taxes increased to $242 billion, up from $181 billion in 2011, largely due to changes in tax rules, The Wall Street Journal noted.
Spending on defense, Social Security, Medicare and Medicaid accounted for about two-thirds of outlays in FY 2012.