The aircraft, from Karachi to Islamabad, had found a thick fog and severe rain near the Pakistani capital.
The pilot lost contact with the control tower in Islamabad during the crash.
Pakistan Interior Minister Rehman Malik said at least five passengers were injured from the rubble and rescue workers to find in the hope that the search further away.
A column of smoke was seen rising from the hills of Margalla after the plane crashed, witnesses said, while rescue workers went to the site.
Officials initially thought it was a small plane. But the police official Mohammed Saeed said later: It seems a great tragedy and that the plane was a passenger plane and could be larger than previously thought.
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Rescue teams were headed to the scene, but the streets were difficult, he said.
The accident happened in the Margalla Hills in Islamabad on a rainy morning