The aircraft disappeared from the radar minutes after it took off from Almaty airport at 7.05 am (01:05 GMT) on its way to the capital Nur-Sultan with 95 passengers and five crew members aboard, the airport authority said in a statement.
It hit a concrete barrier and then slammed into an uninhabited two-storey house near the city's boundary northeast of the airport. Kazakhstan responded to the crash by grounding the Fokker model, which makes up the whole of the Bek Air fleet, and launched an investigation.
The country's emergencies committee released a list of 12 people who died, including the captain. The health ministry said 53 people had been injured, nine of them children, adding that 10 of the adults were in critical condition.
Most onboard were Kazakhs but the injured also included citizens of China, Kyrgyzstan and Ukraine. Ukraine's embassy in Kazakhstan said two of its nationals had spinal injuries but their lives were not in danger. Neighbouring Kyrgyzstan's foreign ministry said its representatives had visited a Kyrgyz woman injured in the crash and her condition was "satisfactory".
China and Russia, Kazakhstan's main political allies, were among those that sent official condolences, along with Pope Francis. Deputy Prime Minister Roman Sklyar said the plane's tail had touched the runway twice during takeoff.
"Either this is a pilot error, or there were technical reasons," Sklyar said at a press conference in Almaty. "The aircraft split into two parts. Most of the passengers who died were in the front part." Russia's pro-Kremlin REN TV channel broadcast what it said was a recording of communications between an air traffic controller at Almaty airport and the Bek Air crew.
Soon after takeoff, the air traffic controller appeared to lose touch with the pilot and warned the next plane to delay its takeoff. "We do not know where the Fokker 100 is located," the air traffic controller said.
President Kassym-Jomart Tokayev pledged to provide families of the victims with compensation and tweeted that those responsible "will be severely punished in accordance with the law." Tokayev also said a government commission had been set up to investigate the circumstances of the crash.
The president's office declared Saturday a national day of mourning. The interior ministry said it had also launched a criminal investigation into the incident over violations of air transport safety rules. While the plane was built in 1996, it had passed safety checks in May, Kazakh authorities said.
The industry ministry said in a statement that the Fokker 100 model, which is no longer manufactured, would be grounded until the cause of the accident became clear. Bek Air describes itself on its website as Kazakhstan's first low-cost airline. In March 2016, a Bek Air Fokker 100 plane with 116 passengers made an emergency landing in Nur-Sultan after its landing gear failed to deploy but no one was injured.
Swiss regional carrier Helvetic Airways phased out its Dutch-built Fokker-100s earlier this year after 15 years of service. The first eight victims died at the scene of the disaster, two then died while being treated at the airport and two in hospital.
Those confirmed dead included the captain Marat Muratbayev, as well as Rustam Kaidarov, a 79-year-old retired general, and 35-year-old Dana Kruglova, a journalist from the private Informburo news agency. Informburo said Kruglova "had wanted to celebrate the New Year with her parents in Nur-Sultan and decided to take this flight".
A well-known entrepreneur, Aslan Nazaraliyev, posted on Facebook that he had survived, indicating his seat on a photo of the crashed aircraft, right next to where it had split into two. "Thanks to Allah, I am alive and well," Nazaraliyev wrote.
The air route between Almaty and Nur-Sultan became Kazakhstan's most popular after the chilly steppe city replaced the southern financial hub as national capital in 1997. Many Kazakhs regularly commute between the two cities, after government offices and large companies moved north to Nur-Sultan, formerly known as Astana before being renamed in honour of first Kazakh president Nursultan Nazarbayev.