A congruence $\varepsilon$ on a semigroup $S$ is perfect if for any congruence classes $x\varepsilon$ and $y\varepsilon$ their product as subsets of $S$ coincides (as a set) with the congruence class $(xy)\varepsilon$. Perfect congruences on the bicyclic semigroup were found in \cite{key7}. Using the structure of bisimple $\omega$-semigroups determined in \cite{key25} and the description of congruences on these semigroups found in \cite{key20} and \cite{key1}, we obtain a complete characterization of perfect congruences on all bisimple $\omega$-semigroups, substantially generalizing the above mentioned result of \cite{key7}.