Abstract The e-beam and radiation wave dynamics in the radiating and non-radiating beam transport sections of Free Electron Lasers are analyzed in the collective regime by use of a single transverse mode linear response formulation. This is employed to derive conditions for coherent operation of seeded high gain FELs. It is shown that the level of incoherent self-amplified spontaneous emission (SASE) radiation power can be controlled by adjusting the plasma oscillation phase in the non-radiating beam transport sections preceding the FEL, and that at short wavelengths the FEL coherence is limited by energy noise (rather than current shot-noise), and ultimately by quantum noise