The Airbus 310-300, owned by Novosibirsk-based S7, formerly Sibir, was making a routine flight from Moscow to the city of Irkutsk, about 3,000 miles east of the capital and the home airport for popular tourist destination Lake Baikal.
But disaster struck flight 788 at 7:44 a.m. local time (10:44 p.m. Saturday GMT) and its 200 passengers and crew.
With prosecutors investigating a technical fault as a possible cause of the tragedy, Transportation Minister Igor Levitin told the Vesti news channel, "The plane landed and the crew told the controller that the landing was over."
He said rain had affected the runway, which could explain why the plane overshot the runway before plowing to the airport fence and then into a collection of garages.
However, emergency services and prosecutors were refusing to rule out other versions.
"According to one of the versions, a fire broke out inside the airbus when the plane landed," a representative of the Emergency Situations Ministry said. "According to another version, the landing gear caught fire during landing."
S7 said the plane was in working order and Airbus said the aircraft, manufactured in 1987, had made more than 10,000 flights and had a flight record of over 52,000 hours.
The ministry also said 54 people were being treated in hospital, including six children. They had been rescued from the plane's tail section, which is virtually all that remains intact. All eight crewmembers are believed to have been killed.
Prosecutors suggested that as many as 150 people could have died and rescuers at the scene have recovered 120 bodies.
President Vladimir Putin expressed his condolences to the families and friends of all those who died and pledged to make all the necessary assistance available.
"The president of Russia expresses his deepest condolences to the families and friends of those people who were killed in the Irkutsk plane crash," the press service said in a statement.
The plane's flight recorders have been recovered and will be sent to Moscow for analysis.
Irkutsk has witnessed other plane tragedies. In January 1994, a Tu-154 aircraft crashed on takeoff from Irkutsk, killing 124 people. Three years later, a military transport plane came down in a residential area killing 76. In July 2001, a Russian-made Tu-154 crashed as it was preparing to land with the loss of all 145 people on board.
