The Afghan government's customs agency is demanding $70 million in fines for U.S. shipping containers that do not have validated customs forms.
The Washington Post quotes U.S. military officials as saying the dispute has halted the flow of U.S. military equipment across Afghanistan's borders and forced the military to rely more heavily on air transport.
They said this change has drastically increased the cost of the U.S. troop withdrawal and, if left unresolved, the situation could raise the cost of the drawdown by hundreds of millions of dollars.
A Pentagon official said that Washington was working to resolve the issue, adding that the U.S. "position on what is appropriate is clear."
An advisor to Afghanistan's finance minister told VOA's Afghanistan service that U.S. forces have not submitted customs exemption papers for 70,000 consignments and that each "administrative shortcoming" came with a $1,000 fine.
He also said the Afghan government was demanding to know what was in each container leaving the country because there were concerns that contractors were trying to smuggle things.
The added expenditure comes at a time when the U.S. military was dealing with steep congressionally-mandated budget cuts.
The dispute also comes as the Obama administration is negotiating a long-term, bilateral security agreement with the Afghan government.