"This was definitely no accident. This was a homicide. What happened in Medellin was murder," Defense Minister Reymi Ferreira told journalists.
The LaMia airlines plane slammed into the mountains outside Medellin last week, killing most of Brazilian football team Chapecoense Real as they traveled to a match.
A harrowing recording has emerged of the pilot radioing the control tower to report he was out of fuel.
Investigations are ongoing, but Colombia's civil aviation safety chief has said the plane disregarded international rules on fuel reserves.
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Ferreira accused the plane's pilot, Miguel Quiroga, who died in the crash, of ignoring regulations requiring him to refuel mid-route.
"Obviously, if the pilot had complied with the regulation, which is to land in Cobija (Bolivia) or Bogota (Colombia), or had at least declared an emergency from the beginning, before he was about to have an accident, it's possible this tragedy would not have happened," he said.
Prosecutors in Bolivia, Brazil and Colombia are carrying out a joint investigation into the crash.