More than 20 heavily-loaded vehicles, including oil tankers, were stranded at the border in Torkham following the government decision.
A senior government official told Pakistan's Dawn news that an order came "from Islamabad and the Frontier Corps has been asked to stop oil supplies to Nato forces forthwith".
But another official told Dawn in Peshawar that no decision to suspend oil supplies had come from Islamabad, saying instead it was taken at the local level in view of increased fighter activities in the Khyber region.
"Why would Pakistan suspend oil supplies due to increased US attacks in the region? It goes against conventional wisdom," he said.
"Torkham highway has become extremely dangerous due to militancy in Jamrud and Landi Kotal. The administration needs to beef up security of the highway.
"When we have enough troops on the ground to ensure safety of oil tankers, the supplies would be allowed to go through," he told Dawn.
Most fuel and other supplies for US forces in Afghanistan are transported through Pakistan, crossing the border at two points - Torkham and Chaman, to the southwest.
The Chaman crossing, where supplies bound for foreign forces in the south of Afghanistan, particularly Kandahar, was operating normally on Saturday.
In April, Russia agreed to allow Nato to transport non-lethal supplies through its territory and into northern Afghanistan.
Wednesday's pre-dawn ground assault on the village of Angor Adda in South Waziristan on the Afghan border was the first known incursion into Pakistan by US troops since the invasion of Afghanistan in 2001.
Pakistani officials said the raid killed 20 people, including women and children.
The US has not officially acknowledged any involvement in Wednesday's raid.
Pakistan's envoy to the US said on Friday the raid had failed to capture anyone important and helped fighters by enraging the Pakistani public.
While Wednesday's attack was the first known ground assault, there have been numerous air attacks within Pakistan, many carried out by US-operated pilotless drone aircrafts.
Two such attacks occurred this week. About nine fighters were killed by missiles fired by suspected drones in the northwest on Thursday and Friday.
General Tariq Majid, chairman of Pakistan's joint chiefs of staff committee, said on Friday that cross-border strikes would alienate ethnic Pashtuns.
The US has claimed that al-Qaeda and pro-Taliban fighters live in sanctuaries in northwest Pakistan's ethnic Pashtun tribal areas, where they organise attacks in Afghanistan.