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The demodulation of ultra-short light pulses with photodetectors is accompanied by excess phase noise at the pulse repetition rate and harmonics in the spectrum of the photocurrent. The major contribution to this noise is power fluctuations of the detected pulse train that, if not compensated for, can seriously limit the stability of frequency transfer from optical to microwave domain. By making use of an infrared femtosecond laser, we measured the spectral density of the excess phase noise, as well as power-to-phase conversion for different types of InGaAs photodetectors. Noise measurements were performed with a novel type of dual-channel readout system using a fiber coupled beam splitter. Strong suppression of the excess phase noise was observed in both channels of the measurement system when the average power of the femtosecond pulse train was stabilized. The results of this study are important for the development of low-noise microwave sources derived from optical "clocks" and optical frequency synthesis.