The debris was found 30km south of where the plane last made contact, the Air Force said in a statement on Wednesday. The parts were being recovered for analysis to determine if they belonged to the Hercules C-130 cargo plane.
The aircraft disappeared shortly after taking off late on Monday from the southern city of Punta Arenas. The Air Force concluded the aircraft must have crashed early the next morning, given the number of hours it had been missing.
"We will continue the search and hope for a better result," Air Force General Eduardo Mosqueira, who leads the search effort, told reporters.
The cause of the crash was unknown and officials acknowledged the slim chances of finding survivors.
Earlier on Wednesday, the Chilean military sent fighter jets in an expansion of its search after large rolling waves in the icy Drake Passage and low clouds had complicated the mission the day before, authorities said.
Mosqueira had said the search area would be expanded for at least the next six days.
"We could add four days and bring this to 10 days, but after that we would need to decide whether or not to continue."
The flight appeared routine until the moment it disappeared, he said.
The region where the plane disappeared is a vast, largely untouched ocean wilderness of penguin-inhabited ice sheets off the edge of the South American continent with depths of 3500 metres (11,500 feet).
The military was using sonar-enabled Navy ships to detect irregularities at depth, and that it had established quadrangles to help organise the search. Ships from Argentina and Brazil were assisting, Mosqueira said.
