The development of physical vapor deposition systems that employ inert gas jets to entrain and deposit atomic and molecular fluxes have created an interest in the atomic assembly of thin films under high pressure (10–500 Pa) deposition conditions. Thin films grown under elevated pressure and low surface mobility conditions can contain a higher volume fraction of porosity and a different pore morphology to coatings created by conventional, low pressure (<10−4 Pa) deposition processes. A recent direct simulation Monte Carlo simulation analysis of binary vapor–gas jet atom interactions has shown that the incident angle distribution (IAD) for vapor atom impacts with a substrate is strongly effected by the background pressure. Here, these results are combined with a kinetic Monte Carlo technique to simulate the high pressure growth of vapor deposited nickel films and identify the mechanisms of pore formation. We find that when the surface atom mobility is low, shadowing of oblique angle arrivals by features on the substrate result in the incorporation of porosity with a hierarchical size distribution that includes elongated, inter-columnar pores and finer scale intra-columnar pores. The nucleation of the inter-columnar pores is related not only to the IAD, but also to the height and spacing of the initial asperities on the substrate and to those that subsequently evolve during deposition. The volume fraction of the inter-columnar pores is found to increase as both the fraction of oblique atom arrivals and the height of the asperities increase. For each prescribed IAD and asperity height, an asperity spacing is found that maximizes the inter-columnar pore fraction. By varying the IAD for a given substrate surface topology, in conjunction with intermittent observations of the coating structure during the growth process, the flux shadowing mechanisms that govern the inter-columnar pore nucleation have been determined.