We present a new method for generating initial conditions for numerical cosmological simulations in which massive neutrinos are treated as an extra set of N-body (collisionless) particles. It allows us to accurately follow the density field for both Cold Dark Matter (CDM) and neutrinos at both high and low redshifts. At high redshifts, the new method is able to reduce the shot noise in the neutrino power spectrum by a factor of more than $10^7$ compared to previous methods, where the power spectrum was dominated by shot noise at all scales. We find that our new approach also helps to reduce the noise on the total matter power spectrum on large scales, whereas on small scales the results agree with previous simulations. Our new method also allows for a systematic study of clustering of the low velocity tail of the distribution function of neutrinos. This method also allows for the study of the evolution of the overall velocity distribution as a function of the environment determined by the CDM field.