With Afghan authorities insisting the United States owes millions of dollars in customs fines and trucks carrying hardware being blocked at border crossings, the Americans have started flying out most equipment by air at great cost.
"The cost is five to seven times more" by aircraft than over land through neighbouring Pakistan, a defense official, who spoke on condition of anonymity, told AFP.
The Afghan government is insisting that US forces pay USD 1,000 for each shipping container leaving the country that lacks what it calls a valid customs form.
The US Congress was warned in May by the special inspector general for Afghanistan reconstruction that Kabul was exacting exorbitant customs fees and taxes in violation of previous agreements regulating imported goods and the status of US forces.
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In some cases, Afghan officials were blocking commercial trucks from delivering food and fuel to US forces due to the customs dispute, the inspector general said.
To collect fines that Washington allegedly owes Kabul, "the only way is to stop all trucks from crossing the border," Najibullah Wardak, the director general of the Afghan Customs Department, told the Washington Post.
The Pentagon in a statement acknowledged "challenges" with the withdrawal at Afghan border crossings.
The disputes are "typically centered on the interpretation of Afghan customs processes," spokesman Lieutenant Colonel Bill Speaks said in the statement.
NATO-led force commanders are talking with Afghan officials and "we are confident that the situation will be resolved soon," he said.
Recent tensions with Pakistan have previously forced the US and its NATO allies to transport large amounts of cargo by air and by a longer, more expensive route through Central Asia.