In this work the stability of the “fast electron beam–gas-discharge plasma” system was investigated within the framework of the kinetic approach and under conditions when the Knudsen number of the discharge is of the order of 1. As shown, the loss of stability of the system with respect to the beam and plasma noise occurs at the same parameters of the system. Thus, when developing the theory of the instability of the “fast electron beam–plasma” system, it is necessary to solve the problem with both initial (for plasma noise) and boundary (for beam noise) conditions. The increment of the amplification of the beam noise at frequencies close to the plasma ones is significantly higher than this value for the plasma noise. Thus, the latter have little effect on the phase focusing process at the linear stage if a plasma frequency is present in the beam noise spectrum.