An Afghan Defence Ministry spokesman on Saturday said no one had been found alive.
"There are no survivors from the crash," he said. "We will begin to evacuate and retrieve the bodies."
The Boeing 737 aircraft, operated by private Afghan airline Kam Air, went missing on a flight from the western city of Herat after it was turned away from Kabul airport on Thursday in a snow storm. It disappeared off radar screens shortly after.
"Dutch AH-64 Apache helicopters that were searching for the missing Kam Air Boeing 737 have found the wreckage at 1.37pm. The wreckage was spotted in the Shaperi Ghar area approximately 30km south-southeast of Kabul city," said a statement from Nato peacekeepers in Kabul.
"The tail of the aircraft was spotted with other debris," it said.
The Nato-led International Security Assistance Force has sent specialist mountain rescue teams to the area.
An Afghan Defence Ministry spokesman identified the crash site as being near Band-e Ghazi, a village overlooked by the mountain of Shapiri Ghar.
Between 80 and 100 Nato troops had been sent out to scour the area where the plane is thought to have crashed.
The Afghan Defence Ministry earlier said two battalions, about 1200 men, were searching within a radius of 60km, near the villages of Khak-e Jabar, Band-e Ghazi and Khurd Kabul, 30km southeast of the capital.
The plane was turned away from
Kabul airport because of snow
A number of foreigners were among the 96 passengers, including nine Turks, three American aid workers, an Italian naval captain, two other Italians and an Iranian working for an international non-governmental organisation.
Six of the eight crew members were also foreigners. The plane was leased from a company in Kyrgyzstan, but Kam Air officials said they could not be sure of the crew's nationalities.
Kam Air opened as Afghanistan's only private airline in November 2003. It flies leased aircraft between Kabul, Dubai and Istanbul and operates several domestic routes.
In September, an Antonov-24 operated by the airline slewed off the runway while landing in Kabul, slightly injuring some of the 27 passengers aboard, apparently after engine trouble.
In early 1998, 51 people died when an Antonov transport plane operated by state-run Ariana Afghan Airlines crashed into mountains near the southwestern Pakistani city of Quetta after failing to land in Afghanistan because of bad weather.
In March that year, 45 people were killed when another Ariana plane, a Boeing 727, slammed into a mountain near Kabul.
In the most recent air crash in Afghanistan, three US military personnel and three civilian crew members were killed when a US transport aircraft crashed in central mountains in November.