AKIPRESS.COM - Nils Kauffman, who served as an education officer for the U.S. Agency for International Development in Afghanistan, said he noticed irregularities at a vocational training institute the agency was funding during his visits to its campus in downtown Kabul in 2012 and 2013. He recalls being surprised not to see any students in the institute’s laboratories, where volt meters and scientific equipment remained in their original packaging.

Though Kauffman spied students elsewhere, he said he could never get a reliable account of how many were actually enrolled at the school. He also could not verify that the institute had addressed what a 2011 external audit called a host of “deviations” from sound practices, including a lack of accounting software, a cash-based payment system, and $118,000 in spending by the school over a five month period on weapons, international travel, and salary supplements.

Kauffman didn’t have the authority to demand a new, broader audit of the institute, but he reported his concerns to his superiors at USAID. They never acted, he said, and he recalls an official in the agency’s Office of Afghanistan-Pakistan Affairs expressing worry that canceling the institute’s funding would create what the official called “bad press.”

“Every time something came up, they jumped to keep this guy [the institute’s leader] happy, despite the problems, despite the lack of financial transparency,” said Kauffman, who is now a private development consultant based in the San Francisco Bay Area. In fact, USAID continued giving the institute funds, totaling at least $12.3 million through last Sunday, according to USAID spokesman Sam Ostrander.

Kauffman’s experience is only a small part of the controversy suddenly surrounding the long-running U.S. effort to promote the education and training of the largely illiterate population in Afghanistan. More than three-quarters of a billion dollars in U.S. funds have been used to finance the effort, and USAID has repeatedly depicted it as one of its signal accomplishments there.

Last month, Afghanistan’s newly-appointed education minister raised questions about the veracity of that claim when he told his country’s parliament that some aid funds had flowed to so-called “ghost schools, which are only on paper,” according to several Afghan media accounts of the May 27 session. The minister, Assadullah Hanif Balkhi, said that officials in the previous government — in power from 2004 to 2014 — lied about the number of schools to obtain more foreign funds.

“It is a fact that there are no schools in some parts of the country, but all the expenses — including teachers’ salaries — are being paid, and now we will bring reforms to this waste,” Balkhi told the parliament, according to Tolonews, a publisher and broadcaster based in Kabul.

Asked to provide more detail, a spokesman for the ministry, Kabir Haqmal, later told NBC News — the Center for Public Integrity's publication partner for this article — that the matter is still under investigation. In some cases, he said, schools may have been closed due to fighting while “permanent absentees” were kept on the books for years, following a requirement of Afghan law.

“There could be schools that do not exist, but we [are] assessing all our records and so far have not found any such instances,” Haqmal said. “That does not mean there are no ghost schools, but we just do not have that information yet. We are taking this very seriously and will share our finding with public very soon."

The new minister’s claims have provoked the top federal auditor for U.S. reconstruction efforts in Afghanistan, John F. Sopko, to express concern that “U.S. and other donors may have paid for schools that students do not attend and for the salaries of teachers who do not teach.”

In a June 11 letter to acting USAID administrator Alfonso E. Lenhardt, released by Sopko on June 18, Sopko said the allegations about “ghost schools, ghost students, and ghost teachers call for immediate attention,” and asked the agency to explain within two weeks what it is doing to investigate the reliability of its data and the potential misuse of its funds.

Accurate data, Sopko said, “is essential for gauging progress in USAID’s education programs and for making future funding decisions.”

USAID spokesman Ostrander, in an emailed response to questions, said the agency will provide a detailed reply to Sopko by the June 30 deadline. According to a written statement Ostrander provided to the Center for Public Integrity from Larry Sampler, assistant to the USAID administrator for Afghanistan and Pakistan, the agency has already asked the Afghan Education Ministry for more information. USAID currently has a full-time employee assigned to help the ministry improve the reliability of its data, according to Sampler’s statement.

Like all the agency’s projects in Afghanistan, “USAID-implemented education projects adhere to the Agency’s strict practices for monitoring their performance and success,” Sampler wrote.

USAID has repeatedly boasted about its role in raising enrollment rates in Afghanistan, citing Afghanistan Education Ministry data. More than eight million Afghan students were enrolled in 2013, compared to just 900,000 in 2002, according to data that Sopko cited in his most recent quarterly report. He said USAID had acknowledged these figures could not be independently verified, however.

At the Afghanistan Technical Vocational Institute, where Kauffman said he observed irregularities, 4,529 students have so far graduated “with the support of USAID and other sponsors,” Ostrander said. But the institute’s founder and director, Sardar Roshan, reached by cell phone in Kabul, told the Center for Public Integrity that the total number was “close to 7,000.” Ostrander told the Center for Public Integrity he could not explain the discrepancy.

This story was published by The Center for Public Integrity, a nonprofit, nonpartisan investigative news organization in Washington, D.C.