An apparatus for controlling operation of an internal combustion engine including a multiplicity of cylinders. The apparatus comprises a control means for detecting speedily reference positions for control of the individual cylinders with high reliability. In the control means, a reference position signal generating means for generating a reference position signal containing six equiinterval rectangular pulses each having a duty cycle of 1/2 during a single rotation of a crank shaft is provided in combination with a cylinder identification signal generating means for generating a plurality of different-interval rectangular pulses during a rotation of a shaft interlocked to the cam shaft so that a series of four successive signal levels of the different-interval rectangular pulses sampled at one edges of the equi-interval rectangular pulses differ from one to another succeeding series. The series of the signal levels thus fetched are stored in a signal level data storage means. A reference position determination unit is provided for generating a decision signal by determining the reference positions for the individual cylinders, respectively, on the basis of the four successive signal levels as stored.