And the office of the Special Inspector General for Afghanistan Reconstruction urged the Pentagon to boost oversight of how US money is being spent, particularly amid moves to direct funds straight to Kabul.
Afghanistan is largely dependent on imports to meet its energy needs, with Russia, Turkmenistan and Iran being its main fuel suppliers.
Accurate data is hard to come by because of unreliable Afghan customs figures, but the State Department told SIGAR that Afghanistan imports between a third and half of all its fuel from Iran.
Between 2007 and 2012, Washington shelled out some $1.1 billion to buy and deliver imported fuel to the Afghan army, Inspector General John Sopko said in his report.
"The fact that the United States has paid for the acquisition and delivery of imported fuel for the Afghan National Security Forces (ANSF)... raises concerns that US funds could have been used to pay for imports of fuel potentially in violation of US economic sanctions against Iran," he wrote.
Iran is under a tough series of US and international sanctions, imposed over its suspect nuclear program and its refusal to stop enriching uranium.
The West suspects Tehran is seeking to build a nuclear weapon, charges denied by the Islamic Republic, which says its program is intended only for medical research and civilian energy purposes.
A certification process was finally put into place in November under which outlets selling fuel to Afghan security forces must clearly state that none of it has come from Iran.
But the Pentagon "lacked certification procedures prior to November 2012 and had limited visibility over the import and delivery sub-contracts used by fuel vendors," Sopko said in the report sent to Defense Secretary Leon Panetta and Secretary of State Hillary Clinton.
"As a result, DoD is unable to determine if any of the $1.1 billion in fuel purchased for the ANA (Afghan National Army) between fiscal year 2007 and 2012 came from Iran, in violation of US economic sanctions."
The inspector general also noted that it will become more difficult for the Pentagon to account for how US funds are used as Washington begins transferring funds directly to Afghan offers starting in March.
"The US government may need to take steps to place safeguards on its direct assistance funding -- over $1 billion alone for ANSF fuel from 2013-2018 -- to ensure that the Afghan government does not use the funds in violation of US economic sanctions," the report warned.