The Suzaku data of the highly variable magnetar 1E 1547.0$-$5408, obtained during the 2009 January activity, were reanalyzed. The 2.07 s pulsation of the 15--40 keV emission detected with the HXD was found to be phase modulated, with a period of $36.0^{+4.5}_{-2.5}$ ks and an amplitude of $0.52 pm 0.14$ s. The modulation waveform is suggested to be more square-wave like rather than sinusoidal. While the effect was confirmed with the 10--14 keV XIS data, the modulation amplitude decreased towards lower energies, becoming consistent with 0 below 4 keV. After the case of 4U 0142+61, this makes the 2nd example of this kind of behavior detected from magnetars. The effect can be interpreted as a manifestation of free precession of this magnetar, which is suggested to be oblately deformed under the presence of strong toroidal field of $sim 10^{16}$ G.
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