Using $(223.7\pm1.4)\times10^6$ J/$\psi$ events accumulated with the BESIII detector, we study $\eta_c$ decays to $\phi\phi$ and $\omega\phi$ final states. The branching fraction of $\eta_c\to\phi\phi$ is measured to be $Br(\eta_c\to\phi\phi)=(2.5\pm0.3^{+0.3}_{-0.7}\pm0.6)\times10^{-3}$, where the first uncertainty is statistical, the second is systematic, and the third is from the uncertainty of $Br(J/\psi\to\gamma\eta_c)$. No significant signal for the double OZI-suppressed decay of $\eta_c\to\omega\phi$ is observed, and the upper limit on the branching fraction is determined to be $Br(\eta_c\to\omega\phi)<2.5\times 10^{-4}$ at the 90% confidence level.