The cost of providing security for U.S. development work in Afghanistan will increase sharply as program managers are forced to rely on an Afghan government-run security enterprise, according to the preliminary findings of a U.S. government audit.

The transition, which is off to a rough start, is a key test of the Afghan government’s ability to take on more responsibility for security as U.S.-led NATO forces move ahead with their exit plan.

Steven J. Trent, the acting Special Inspector General for Afghanistan Reconstruction (SIGAR), said in a letter to the U.S. Agency for International Development that the “rushed approach” the U.S. government was taking to comply with new Afghan government rules for private security raised concerns that warrant immediate attention.

The auditor’s analysis found that the cost of Afghan guards that provide security for U.S.-funded projects could increase by as much as 46 percent. Trent also wrote that if the Afghan Public Protection Force, or APPF, was not “fully-functioning” by the March 20 deadline to disband private security companies, USAID projects worth $899 million were at “significant risk of termination.”

In an unusually sharp rebuttal to the auditor’s findings, S. Ken Yamashita, USAID’s mission director in Kabul, said the agency rejected the report “in its entirety.” He challenged SIGAR’s methodology, saying it relied on “inadequate comparisons, speculative assumptions and inaccurate statements.”

The conflicting assessments of the transition to Afghan-run security, and interviews with people who have followed the issue closely, underscored how much anxiety the changeover is causing at a pivotal time in the Afghan conflict. The extent to which U.S. development projects succeed over the next two years will shape the legacy of a decade-long foreign military intervention that has been beset by a series of missteps and growing disapproval for the war among Americans.

The House Committee on Oversight and Government Reform is scheduled to hold a hearing on the security transition on Thursday.

The Afghan government has failed to build the 25,000-guard force it set out to recruit a year ago to comply with President Hamid Karzai’s mandate to disband security companies, which he saw as an affront to Afghan sovereignty. It currently has roughly 6,000 guards on staff, but most of those are already assigned to sensitive installations, such as banks.

At least 32 projects funded by USAID have agreed to adopt the APPF model, although some have said the move could significantly imperil their ability to operate safely in Afghanistan, U.S. embassy officials in Kabul said. Because the Afghan government is not yet in a position to assign trained guards to new sites, for the time being, most project managers are keeping their own guards.

The American University of Afghanistan, which is among the entities that receives U.S. funding and is adopting the new security system, said in a letter to its staff this month that it anticipates its security apparatus will remain relatively intact.

Afghanistan’s new security structure nominally took effect March 20, although the Ministry of Interior, which runs the APPF, has agreed to extend the licenses of some private security companies for a few weeks.

The ministry will charge clients for firearms, ammunition, training, uniforms and administrative costs, SIGAR’s report said. The government will also seek to make a profit from the state-run company, although Deputy Interior Minister Jamal Abdul Naser Sediqi, who oversees the APPF, said in an interview that it is too early to tell how much money will go to the government’s coffers.

Based on information provided by USAID, SIGAR calculated that the net cost of an Afghan guard would be between $710 and $830 per month, an increase of between 25 and 46 percent. SIGAR said some project managers anticipate they will have to hire more expatriate security experts in the short term to manage the transition.

Several foreign security companies have registered as risk mitigation companies with the Ministry of Interior to remain in the lucrative business. The ministry is charging a $120,000 yearly licensing fee and demanding that each firm deposit $400,000 in a bank account, which the government can tap into if it sees fit to impose fines on the companies.

USAID said in a written response to SIGAR that it disagreed with the audit’s guard cost calculations. U.S. officials acknowledged, however, that they don’t yet know what the cost difference will be. Based on the estimates of four project managers who offered feedback on the transition, the cost hike is likely be closer to 16 percent, a U.S. official said during a briefing the American Embassy arranged on condition that the officials not be named. Officials described that as an initial estimate and said they think security costs could eventually drop once there are more licensed foreign risk management companies to bid on contracts.

“The transition is happening as planned, but not without challenges,” one official said. “We’re feeling confident in the progress that has been made, although we recognize there are operational issues to work through.”