"On January 18 at 10:30 am (0430 GMT), a bus caught fire ... 55 passengers and two drivers were on board. Five people who managed to escape are receiving medical assistance. The rest died on the spot," the ministry said, without elaborating on the cause of the blaze.
All those who died are believed to be Uzbek nationals, an interior ministry official told Interfax-Kazakhstan news agency. Kazakh media reported they were migrant workers travelling to Russia.
The vehicle was registered in Kazakhstan, emergency services ministry official Ruslan Imankulov told AFP. He said the fire spread very quickly.
Regional emergency service officials initially blamed the fire on a short circuit and said the bus was overloaded, Interfax-Kazakstan news agency reported.
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Ministry representative Imankulov did not confirm this however, telling AFP: "It's too early to talk about the reasons for the fire."
Panic broke out on board the bus, hindering evacuation, while survivors managed to climb through a door and window, Kazakh news site BNews reported.
Two of the survivors suffered burns to their hands, emergency services officials told AFP, while others suffered minor injuries.
Video broadcasts by Russian and Kazakh media showed black smoke and flames billowing from the vehicle which had veered across a flat stretch of road carving through a snowy steppe. A photograph taken later showed the vehicle completely charred.
The ministry said the vehicle was a Hungarian-made Ikarus. These buses are still widely used in ex-Soviet nations, even though they are often decades old.
The accident is one of the deadliest in the last five years, with the worst toll in Afghanistan in 2016 when two buses collided with an oil tanker, killing at least 73 people.
In October last year, a Kazakh-registered bus with Uzbek passengers was hit by a train in Russia after breaking down on the tracks, killing 19 aboard the bus.
In 2015, 16 people, including three children, died in Kazakhstan when a minibus collided with a van on April 20, 2015.