To ensure safe passage through dangerous areas, the trucking companies make payments to local security firms with ties to the Taliban or warlords who control the roads.
If the payments are not made, the convoys will be attacked, according to the document detailing the allegations.
The document also says the companies hired under the Afghan Host Nation
Trucking contract may be paying between $2m and $4m per week to armed groups.
The Host Nation Trucking contract is an essential part of the effort to sustain more than 200 US military combat outposts throughout the country.
|The US military relies on logistics contracts to sustain their combat bases [AFP]
Supplies are usually shipped through Pakistan to Bagram Airfield, the US military's main base in Afghanistan, and then on to the outlying bases.
One of the security firms under scrutiny is Watan Risk Management, one of the country's largest security providers.
According to the document, Watan representatives allegedly negotiate or dictate the price for security in a certain area, as well as warning trucking companies that are late in paying or refuse to do so.
Meanwhile, a US congressional subcommittee also conducted its own investigation into the trucking contract.
Its report, released on Monday, says the trucking contractors pay tens of millions of dollars annually to local warlords across Afghanistan in exchange for guarding their supply convoys.
"Although the warlords do provide guards and coordinate security, the contractors have little choice but to use them in what amounts to a vast protection racket," the report said.
The consequences are clear - trucking companies that pay the highway warlords for security are provided protection [and] trucking companies that do not pay believe they are more likely to find themselves under attack. As a result, almost everyone pays."
The report also said that armed groups are not the only beneficiaries.
One security company told the subcommittee that it had to pay $1,000 to $10,000 in monthly bribes to nearly every Afghan governor, police chief and local military unit whose territory the company passed through.
Bribes and kickbacks are often part of the business environment in Afghanistan.
Last year, at a Senate Armed Services Committee hearing, Hillary Clinton, the US secretary of state, acknowledged the long, rugged supply lines to Afghanistan through Pakistan's port city of Karachi offer numerous opportunities for fraud and corruption.