Involuntary respiration is controlled by the respiratory centres of the upper brainstem. This region of the brain controls many involuntary and metabolic functions besides the respiratory system. The medulla oblongata is the primary respiratory control center.
This is the case of human respiratory system. Similarly there will be a control mechanism for breathing for every other organisms.
The respiratory tract is divided into two parts, upper and lower parts.
Upper part consists of nose, nasal cavities and upper pharynx. The lower part contains the lower part of pharynx.
So the process is under the control of the brain.