The incident occurred Monday at 8:35am in the town of San Francisco de Río Tinoco in Palmar de Osa, Puntarenas.
Captain Alex Ulloa and copilot Jose Luis Vargas Salas piloted the aircraft. Both were unharmed.
The helicopter departed from the base of the Air Surveillance Service of the Ministry of Security at the Juan Santamaria Airport in Alajuela at 7:15am, en route for Punta Burica, near the border with Panama.
The captain, who has 34 years experience as a pilot, said while traveling at 3,000 feet he noticed a burning smell, and immediately began to lose power to the motor.
The captain said the aircraft had just been returned on Monday after undergoing repairs.