Images from the scene showed civilians clambering around the broken tail of the aircraft, marked FAC 1016, as smoke and flames billowed above the trees.
Defence Minister Pedro Sanchez expressed “deep sorrow” over the disaster.
“Military units are already at the scene,” Sanchez posted on social media, adding that “the number of victims and the causes of the crash have not yet been confirmed”.
“It is a deeply painful event for the country. May our prayers bring some measure of comfort,” said Sanchez.
General Carlos Fernando Silva Rueda said that 114 troops were aboard and 11 crew.
They had been travelling between Puerto Leguizamo and another Amazon outpost nearby.
The crash is the second by a C-130 Hercules aircraft in South America in under a month.
A Bolivian military cargo plane carrying banknotes crashed while landing near La Paz on February 27, killing at least 24 people.
The Hercules is a four-engine turboprop plane built by Lockheed Martin.
Renowned for its ability to operate from makeshift airstrips, it is widely used by militaries around the world and can carry everything from troops to vehicles.
-Agence France-Presse