The planes and helicopters are intended for the Afghan Special Mission Wing (SMW), but the audit found the unit has no command structure.
And only seven of its Afghan pilots were trained to fly with night-vision goggles, according to the report.
It could take 10 years before the unit is self-sufficient, said the watchdog.
The audit also noted the US currently carried out most of the aircraft repair and maintenance for the Afghans.
‘Waste of US funds’
The Special Inspector General for Afghan Reconstruction’s report found the Afghans could not carry out counter-militancy missions as most of the SMW’s 47 pilots could not fly at night.
The audit also cited difficulties in finding candidates who were literate and able to pass the exhaustive 18-20 month US vetting process.
“The Afghans lack the capacity – in both personnel numbers and expertise – to operate and maintain the existing and planned SMW fleets,” the report said.
As a result, the planes “could be left sitting on runways in Afghanistan, rather than supporting critical missions, resulting in waste of US funds”, the audit said.
“We maintain that moving forward with the acquisition of these aircraft is imprudent,” it added.
The Pentagon has a $218m contract with Nevada-based Sierra Nevada Corporation for 18 PC-12 fixed-wing aircraft and a $554m deal with a Russian firm, Rosoboronexport, for 30 Mi-17 helicopters, according to the audit.
The report recommended the purchases be halted, but Deputy Assistant Defence Secretary Michael Dumont said that would “unacceptably delay our efforts to develop the SMW into a capable force”.