Imperfect atomic state preparation in an optically pumped beam resonator results in over-Poissonian fluctuations of the fluorescence emission of residual unpumped atoms. This excess noise is induced by the frequency noise of the pump laser. We evaluate it theoretically for a three-level atomic system interacting with a noisy laser field, and show that it is predominant within a large range of pumping efficiencies and laser linewidths for usual atomic fluxes. Experimentally, extra noise is detected from ratios of unpumped atoms as low as 0.01% of the atomic flux equal to . This noise source debases the short-term stability of an atomic clock in a flop-in configuration if the proportion of unpumped atoms exceeds 1% of the global atomic flux. In a flop-out configuration this excess noise would decrease the clock stability from a proportion of unpumped atoms of 0.01%.
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