Abstract We analyze contributions to the heavy vector meson production with large transverse momentum in proton-proton and diffractive photon-proton scattering driven by an exchange of two Balitsky-Fadin-Kuraev-Lipatov Pomerons in the squared amplitudes. The Pomerons couple to a single parton and form a Pomeron loop closed by the vector meson impact factors. For the photon-proton case the diffractive cut of the Pomeron loop contributes, and for the inclusive hadroproduction one finds the loop with two cut Pomerons. We compute both of these Pomeron loop contributions and study in detail their properties. The results are then used to calculate the cross sections for diffractive J/ψ photoproduction with large transverse momentum at HERA and the correlated two Pomeron contribution for inclusive J/ψ and ϒ production cross sections at the LHC. Within a unified approach a good description of the photoproduction data is found, but correlated two Pomeron mechanism gives only a small contribution to hadroproduction of the vector mesons at the LHC.