The alert from the office of the Special Inspector General of Afghanistan Reconstruction (SIGAR) is only the latest warning about questionable reconstruction spending in that country. Earlier this year, the agency issued a quarterly report detailing special projects funded by the State Department, the Defense Department and the U.S. Agency for International Development that it investigated and found to be incomplete, badly constructed or, in one case, not even wanted by the U.S. military.

As the United States begins to wind down its 13-year occupation of Afghanistan, an accounting of where the money has gone and whether it has been spent in a meaningful and substantive way is in full swing. The U.S. government has spent more than $80 billion on Afghanistan's reconstruction since it invaded the country in 2001. Half of that has gone to setting up and maintaining the country's police and military. Another $20 billion remains in the coffers amid concerns from both SIGAR and observers in Congress over how the money will be spent, whether the projects can be verified and even whether they can be sustained in a degenerating security environment with fewer U.S. troops on the ground expected by the end of the year.

"If anything, I tell people reconstruction becomes more important from a policy point of view," said Sopko. "Our stated policy for being there is to make certain Afghanistan never becomes a place where it can be a base for terrorist attacks against the United States and its allies." The U.S. military will largely be gone by 2015, he said, "so we've got to get Afghanistan reconstruction right if we really want to make a difference in the future."

The cost of the U.S. war in Afghanistan has already topped $700 billion. Together with the expense of the invasion into Iraq and the subsequent occupation, the bill to American taxpayers stands at more than $1 trillion and counting. In 2011 the Commission on Wartime Spending estimated that as much as $60 billion of U.S. spending in Iraq and Afghanistan had been lost to waste and fraud.

It's not even certain the incoming Afghan government will sign a bilateral security agreement after the April elections. If it does, a residual U.S. military force will remain. If the agreement isn't signed, even that smaller presence isn't guaranteed. And with opposition from the Taliban and with other militant groups waiting to exploit security vulnerabilities, the sustainability of million-dollar projects continues to present major challenges for the U.S. government.