The missing money was part of the relatively small amount of Afghanistan spending that was routed directly to military officers in a bid to bypass bureaucracy and rush the construction of urgently needed roads, bridges, schools, hospitals, water treatment plants and other essential infrastructure. About 70 percent of the $100 billion the United States has spent to rebuild Afghanistan during more than 13 years of war went through the Pentagon, with the rest distributed by the U.S. Agency for International Development and other civilian departments.

A year-long investigation by John F. Sopko, the U.S. special inspector general for Afghanistan reconstruction, found that the Pentagon couldn’t – or wouldn’t – provide basic information about what happened to 6 in 10 dollars of $2.26 billion it had spent over the course of a decade on the Commander’s Emergency Response Program.

“In reviewing this data, SIGAR found that the Department of Defense could only provide financial information relating to the disbursement of funds for CERP projects totaling $890 million (40 percent) of the approximately $2.2 billion in obligated funds at that time,” Sopko’s report says.

When Sopko’s staff divided the Pentagon expenditures into 20 categories set under the emergency program, from transportation and education to health care, agriculture, water and sanitation, by far the largest category was a 21st that the inspector general termed “unknown.”

That category applied to 5,163 projects, compared with 4,494 projects in the 20 defined areas.

The Pentagon didn’t respond to Sopko’s main findings in comments he’d sought while conducting the probe, which were released along with his report on the investigation.

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In one comment, however, U.S. Central Command, which oversees military operations in Afghanistan and 19 other countries in the Middle East and Central Asia, suggested that some of the money was redirected from reconstruction aid to more direct war needs.

“Although the (inspector general’s) report is technically accurate, it did not discuss the counterinsurgency strategies in relationship to CERP,” the Central Command said in a Feb. 25 email to Sopko’s office. “In addition (to) the 20 uses of CERP funds, it was also used as a tool for counterinsurgency.”

The comment didn’t explain why money set aside for reconstruction needs would need to be used to pay for counterinsurgency, which has been a core part of the U.S. military campaign in Afghanistan since the October 2001 invasion following the Sept. 11 terror attacks. The bulk of the Afghanistan war’s $800 billion price tag for the United States has gone to battlefield needs.

Counterinsurgency is not among the 20 categories defined by Pentagon regulations under the emergency-response program. The closest categories to anything battle-related are “condolence payments” to Afghan civilians, or their families, who died or were injured because of the war and “hero payments” to the surviving spouses or next of kin of Afghan soldiers or police killed in the conflict.

The inspector general’s report suggests how intertwined U.S. military and reconstruction efforts in Afghanistan became, and how difficult it is to separate the two.

While Sopko found that Commander’s Emergency Response Program money was disbursed for projects throughout virtually all of Afghanistan’s 35 provinces, almost half of it went to the two – Kandahar and Helmand – that have seen the most Taliban activity and the war’s bloodiest battles.

A total of 1,507 American service members have perished in Kandahar and Helmand, almost two-thirds of all 2,357 U.S. fatalities in the war.

Kandahar, dominated by ethnic Pashtuns on the Pakistan border in southern Afghanistan, has been a Taliban hub since the insurgents took it over in 1994 during the civil war that followed Soviet occupation of the Central Asian country.

About $289 million, almost one-third of the CERP money the Pentagon could account for, was spent in Kandahar, according to the inspector general’s report.

The special inspector general for Afghanistan reconstruction, a post Congress established in 2008 to track U.S. nonmilitary aid to Afghanistan, has issued dozens of reports documenting billions of dollars lost to waste or corruption. In a report released last July, Sopko and his staff found that many of the tens of thousands of excess AK-47 assault rifles and other weapons the Pentagon had shipped to Afghanistan since 2004 had gone missing, raising concerns that they’d fallen into the hands of Taliban or other insurgents.

A report released in October 2013 concluded that the United States was continuing to give Afghan security forces a planned $1.4 billion to buy gasoline through 2018 despite evidence that some of the money had been siphoned off for other, unexplained, uses.

Annual spending on the Commander’s Emergency Response Program peaked in 2009 at $500 million, or 23 percent of its total disbursements over the decade. It was in that year that newly elected President Barack Obama sent additional troops to Afghanistan, fulfilling a campaign promise.

The end of 2009 was also when CERP’s operating procedures were brought into alignment with a broader U.S. program called Afghanistan First, which “encourages the use of Afghan contractors to the greatest extent possible,” according to the new inspector general report.

The number of U.S. troops in Afghanistan peaked at 100,000 in August 2010. Only 9,800 remain, although Obama has slowed his withdrawal plan, promising the Afghan government to keep that number there through this year and delaying the final exit to 2017.

Email: jrosen@mcclatchydc.com; Twitter: @jamesmartinrose