The official said the fees were designed to both express continued anger over the Nov. 26 attack and raise funds for the state to fight homegrown Taleban militants.
No date was given for reopening the supply routes.
The NATO attack plunged relations between troubled allies Pakistan and the United States to their lowest point in years.
Ties had already been severely strained by a secret raid by US special forces that killed Osama Bin Laden on Pakistani soil in May last year, embarrassing the military, which has ruled the country for over half of its 64-year history and sets security and foreign policy.
Asked if the re-opening was a sign that the crisis in relations had eased, the official said there was still some way to go before normalcy was possible.
The two land routes to Afghanistan through Pakistan account for just under a third of all cargo that the NATO-led International Security Assistance Force (ISAF) ships into Afghanistan.
