“Police found the body of the elderly nun in Nangeni in a small stream in the veld,” Colonel Mzukisi Fatyela said before 2pm.
“We are at the scene now waiting for the investigation teams and have not touched the body.”
The nun was hijacked and kidnapped in Norwood in Mthatha on Sunday, he said.
The nun’s car was later spotted in Mthatha by people who worked with her and they followed the car.
“The police were also following the car and as the police approached the car it overturned,” he said.
“Two men escaped on foot and police found a 9mm pistol with five rounds and a cellphone that belonged to one of the men.”
He said the nun was missing and her body was found on Monday afternoon.
Fatyela said investigations continue and no arrests have been made.
The cause of death was not known.