The Fokker 100 aircraft, operated by Bek Air, got into trouble shortly after departing from Almaty, the Central Asian country's commercial center, on a pre-dawn flight en route to the capital Nur-Sultan.
It lost altitude during takeoff and broke through a concrete fence before hitting the two-story building, Kazakhstan's Civil Aviation Committee said. It was not immediately clear what caused the crash.
"Before crashing, the aircraft touched the runway with its tail twice, the gear was retracted," Deputy Prime Minister Roman Sklyar told reporters.
"A commission... will establish whether this was pilot error or technical issues. The runway was in an idea condition."
A Reuters reporter saw the battered remains of the front of the plane and other separate parts of the fuselage scattered around the wreckage of what was left of the house.
A survivor told news website Tengrinews she heard a "terrifying sound" before the plane started losing altitude.
"The plane was flying at a tilt. Everything was like in a movie: screaming, shouting, people crying," she said.
Almaty heathcare authorities initially put the death toll from the crash at 15 or more but later revised the figure down to 12. They said 66 people were taken to hospital, some of them in a serious condition.
The plane had been carrying 93 passengers and five crew, and Kazakhstan's interior ministry said the captain was among those killed.
The ministry said it was investigating a possible breach of flight operation and safety rules, a standard legal procedure. There was thick fog in the area at the time of the crash.
Kazakhstan's aviation committee said it was suspending all flights by carrier Bek Air and those of Fokker 100 aircraft pending the results of the investigation.
"FALLING... AT AN ANGLE"
Another survivor, businessman Aslan Nazaraliyev, told the Vremya newspaper that the plane started shaking while gaining altitude about two minutes after takeoff.
"At some point we started falling, not vertically, but at an angle. It seemed like control over the plane had been lost," he said.
Authorities cordoned off the crash site in the village of Almerek, just beyond the end of the runway.
The airport remained operational with other planes seen taking off after the crash.
In the airport at Nur-Sultan, relatives of the passengers - some of whom were going to reunite with their families for the holidays - were being briefed on their fate and offered flights to Almaty.
"Those responsible will face tough punishment in accordance with the law," Kazakh President Kassym-Jomart Tokayev tweeted, expressing condolences to the victims and their families.
Tokayev declared Dec. 28 a national day of mourning and appointed Prime Minister Askar Mamin to head a commission to investigate the crash.
The plane involved in the crash was built in 1996, the government said, and its most recent flight certificate was issued in May 2019.