Television pictures showed a towering inferno after militants targeted the convoy with gunfire and indiscriminately torched vehicles.
"Seven deaths have been confirmed. Four are injured. There is no information about any arrests," said police official Gustasab Khan. The casualties were the drivers of the trucks, their helpers or local people, he said.
Police could not give a breakdown on the number of tankers and containers destroyed as the Nato vehicles were parked at a depot with other cars.
"Unknown attackers opened fire on vehicles parked at Tarnol. Fire erupted in the tankers and trucks, and over a dozen were set ablaze. They were trucks carrying Nato supplies," said police official Tahir Riaz.
Kalim Iman, inspector general of Islamabad police, told reporters that 10 to 12 attackers had stormed the terminal and then managed to escape, but declined to put a precise figure on the losses.
"Fire has destroyed a number of oil tankers and trailors. We are collecting details. The attackers have been identified. They came on motorbikes and pick-up trucks. They were armed," he said. "We have launched an investigation. Police are trying to arrest them."
Although militants have routinely attacked supplies for US and Nato-led foreign forces fighting the Taliban in Afghanistan, the assault was one of the worst and underlines insecurity on the doorstep of the heavily-guarded capital.
The attacks began as retaliation over a government siege on a radical mosque in Islamabad and flared last year as the military fought campaigns against Taliban in the northwest regions of Swat and South Waziristan.
Although there was no immediate claim of responsibility, similar assaults in the past have been blamed on Taliban fighters.