We employ an optical pump-probe technique to study coherent phonon oscillations in Ca$_2$RuO$_4$. We find that oscillation-amplitude of an $A_g$ symmetric phonon mode is strongly suppressed at 260 K, a putative transition point of orbital ordering. The oscillation also shows a gradual but huge change in its $phase$, such that the oscillation even flips over with a 180$^{circ}$ change across the temperature. Density functional theory calculations indicate that the $A_g$ phonon has an eigenmode of octahedral distortion with conventional tilting along the $a$-axis and antipolar distortion of apical oxygen. Careful inspection of the lattice captures an unusually large antipolar distortion in low-temperature structures, which may play a crucial role for the phase transition at 260 K.
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