The complex admittance of various molecular junctions based on long alkyl chains (C18) has been measured and resolved into different components. The dipolar contribution of the response function has been analyzed in terms of the generalized Langevin equation. This formalism allows us to extract from experimental data the spectral density of polarization noise and to characterize the fluctuation dynamics of the molecules around their equilibrium positions. This spectral density is of $1/f$ type, characteristic of fractional Gaussian noise. It is suggested that the structural disorder of the junctions is at the origin of these polarization fluctuations. Possible relation between the $1/f$ tunnel current and polarization noises is also discussed.
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