Photographs of the wreckage on the internet appear to show the North Korean air force emblem beneath the aircraft's tail.
South Korea's military said the plane was likely a MiG-21, citing radar detection by its air force of the aircraft leaving a military airbase in the North Korean city of Sinuiju, near the border with China.
"Radar images show the North Korean aircraft took off from the air base in Sinuiju," an official in Seoul, who asked not to be named, was reported to have said.
"According to the images, it appears to be a MiG-21," the official said.
South Korea's Yonhap News Agency cited an unnamed intelligence official as saying the pilot may have been attempting to defect to Russia.
The aircraft was said to have ploughed into an apple orchard in a village, about 150km from the North Korean border on Tuesday, killing its pilot.
"The engine was making a very strange noise and it was flying in a very weird way, with it's head up and rear down"
a local witness
A witness said he saw the plane flying low over the area before it crashed.
"The engine was making a very strange noise and it was flying in a very weird way, with it's head up and rear down,", a man named Ning was quoted by The Associated Press news agency as saying.
"It looked like a piece of scrap iron flying in the sky."
He said that he heard from other villagers that the aircraft had flown from North Korea and that the pilot was killed on impact.
China is a neighbour and close supporter of North Korea, which depends on Beijing for food and energy aid.
However, ties have been strained in recent years, particularly since the North resisted an international effort led by Beijing to persuade it to give up its nuclear weapons programme.
In recent years, thousands of North Koreans facing hunger and difficult living conditions at home have made the risky journey into China, with many seeking eventual asylum in South Korea.
The Chinese government has not yet commented on the crash.