We construct and investigate a short exact sequence of Poisson $\mathcal{VB}$-groupoids which is canonically related to the Atiyah sequence of a $G$-principal bundle $P$. Our results include a description of the structure of the symplectic leaves of the Poisson groupoid $\frac{T^*P\times T^*P}{G}\rightrightarrows \frac{T^*P}{G}$. The semidirect product case, which is important for applications in Hamiltonian mechanics, is also discussed.