"Foreign assistance is not a giveaway. It's not charity. It is an investment in a strong America and in a free world," Kerry said at the University of Virginia.
An administration official, who asked not to be named, said that even White House operations will be not spared under the cuts.
Pentagon Comptroller Robert Hale said there would be "very limited exceptions" to the furloughs, including civilians in combat zones, foreign civilians at overseas bases, some police and healthcare workers and political appointees exempted by law.
Hale declined to estimate what percentage of the civilian workers were likely to be furloughed but said it would be more than half. Another defense official said, "we expect more than 80 percent to be furloughed."
The unpaid leave, which will essentially cut the pay of civilian employees by 20 percent, is expected to save up to $5 billion, one of many cuts required as the Pentagon tries to slash $46 billion in spending by the end of the year.
The across-the-board cuts, known as sequestration, are due to take effect on March 1 unless Congress decides to delay them. They were mandated by the Budget Control Act of 2011 because lawmakers and the White House failed to reach a compromise on alternative spending reductions.
The Defense Department, which had warned for weeks about the furlough plan, has imposed a hiring freeze on civilian personnel and ordered the termination of many of its 46,000 temporary and contract workers. Officials said about 6,000 had already been laid off, with more likely to come.