Let $X$ be a finite set. We determine the diameter of the commuting graph of the partial transformation semigroup $\mathcal{P}(X)$ on $X$ and show that it coincides with the diameter of the commuting graph of the transformation semigroup $\mathcal{T}(X)$ on $X$, which was previously determined by Araújo, Kinyon and Konieczny. This proves the existence of a semigroup $S$ and of a proper subsemigroups $T$ of $S$ such that the diameters of the commuting graphs of $S$ and $T$ are equal.