Millions of dollars in US aid is flowing into Afghanistan even though the ministries receiving the funds are incapable of managing such large sums of money, according to a US report.

Despite moves by the US Agency for International Development to boost safeguards over direct assistance to the Afghan government "a number of troubling issues remain," the official report has said.

The US has committed $1.6bn in direct aid to the Afghan government this year to fund 18 programs across ten ministries.

But according to the Special Inspector General for Afghanistan Reconstruction: "USAID contractors assessed 16 Afghan ministries and found they are unable to manage and account for funds."

"USAID's own risk reviews of seven Afghan ministries concluded each ministry is unable to manage US direct-assistance funds," it added, also pointing to a high level of corruption among Afghan officials.

Despite its findings, USAID "waived its own requirements" for direct assistance and has "not required the Afghan ministries to fix most of the risks identified prior to receiving US money."

The watchdog also maintained that USAID had sought to hide its findings from Congress, which is responsible for setting US budgets.

But State Department spokeswoman Jen Psaki hit back, saying that "there are not billions of US assistance dollars going straight into Afghan government coffers".

"On the contrary, we have disbursed less than $300m through rigorous accountable mechanisms that maintain US government control of funds throughout the process," she told reporters.

A later State Department statement said: "We disagree with the impression left by the SIGAR audit report, and conveyed in some of the surrounding media and social media campaign, that [government] funds are being subjected to unnecessary risk in Afghanistan because of the deficiencies identified in the Afghan ministries.

"While there is no way to completely eliminate risk, USAID applies stringent oversight and accountability mechanisms to ensure that its assistance to the Afghan government is implemented properly," the statement added.

It stressed that "the audit report makes no finding of waste, fraud, or abuse in the implementation of direct assistance in Afghanistan".

The audit comes amid a standoff between the US government and Afghan President Hamid Karzai over a security pact to safeguard any US troops remaining in the country after international combat forces are withdrawn at the end of this year.

Mr Karzai is refusing to sign the deal painstakingly drawn up over months with US Secretary of State John Kerry, in a move which the US says jeapordises proper planning for a withdrawal.

The audit by the watchdog, known as SIGAR, may well exacerbate the situation as Mr Karzai has long accused the US of trying to undermine his authority.

SIGAR recommended that USAID should draw up a risk mitigation plan for each Afghan ministry.

But Ms Psaki said that trying to "fix every problem in each ministry before we set up programs" was "not prudent use of US government resources".