The evolution of the Solar System has been shown to be chaotic, which limits our ability to retrace the orbital and precessional motion of the Earth over more than 35-50 Myr (ref. 2). Moreover, the precession, obliquity and insolation parameters can also be influenced by secular variations in the tidal dissipation and dynamical ellipticity of the Earth induced by glacial cyclicity and mantle convection. Here we determine the average values of these dissipative effects over the past three million years. We have computed the optimal fit between an exceptional palaeoclimate record from the eastern Mediterranean Sea and a model of the astronomical and insolation history by testing a number of values for the tidal dissipation and dynamical ellipticity parameters. We find that the combined effects of dynamical ellipticity and tidal dissipation were, on average, significantly lower over the past three million years, compared to their present-day values (determined from artificial satellite data and lunar ranging). This secular variation associated with the Plio-Pleistocene ice load history has caused an average acceleration in the Earth's rotation over the past 3 Myr, which needs to be considered in the construction of astronomical timescales and in research into the stationarity of phase relations in the ocean-climate system through time.