Twenty-seven people were on the flight, which went down near the city of Shymkent, officials said.
A regional emergencies head told Ria news agency the plane had been completely destroyed.
The Antonov An-72 plane was carrying border service officers, including acting head Turganbek Stambekov.
KTK TV said the plane had disappeared from radar shortly before 19:00 Kazakhstan time (13:00 GMT) as it was making its descent near Shymkent, which is the main Kazakh city in the south, some 75 miles (120km) north of the Uzbek capital, Tashkent.
Eyewitnesses told KTK that the plane fell from a height of 800 m (2,600 ft), causing a loud explosion.
A resident identified as Baurzhan Dosov described a big fire, adding that military hats were strewn around the crash site.
The plane went down 12 miles (20 km) from Shymkent aiport in what correspondents told KTK was very bad weather.
“There was no need for rescuers’ help. Only fragments remain,” the head of Kazakhstan’s regional emergencies department, Valikhan Derezhepov, told Ria news agency.
Seven crew and 20 military personnel were on board the military transport plane, Kazakhstan’s Committee for National Security said in a statement.
Interfax-Kazakhstan said that one of Col. Turganbek Stambekov’s deputies and several regional border service commanders were also on the flight, from the Kazakh capital, Astana, to Shymkent.
Col. Turganbek Stambekov was made acting head of the service in June, weeks after 14 border troops were found dead at a burnt-out border post near Kazakhstan’s southern frontier with China. The incident prompted his predecessor to resign.
Another border guard was jailed for life for his alleged role in the incident at the Arkankergen post near Almaty, after he had reportedly confessed to the authorities.
He later said he had been forced into making the confession.
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