Closing the crossings will choke off almost half of all supplies destined for the Nato-led force.
Accounts still differ about what actually happened in the early hours of Saturday morning when American aircraft attacked two border posts on Pakistani soil.
However, no one doubts that the incident has taken US-Pakistani relations close to collapse.
Pakistan immediately shut its borders to convoys taking fuel and supplies to forces in Afghanistan and says it is reviewing all military and diplomatic ties with the US and Nato.
Last year the main crossing between the two countries was shut for 11 days but reopened when the US apologised for an attack that killed two Pakistani personnel.