In the context of high level radioactive waste deep geological disposal safety calculations, flow and radionuclide transport calculations are of first importance due to the time scale of million years as well as the hundreds of cubic kilometres of geological media to be considered. Geological disposal system is composed of waste canisters of meter extension inserted in repository cells and connecting galleries system of tens to hundreds of meter extension themselves embedded in the geological formation of kilometre extension. Geological layer of interest in France is a clayey formation of very low permeability (of the order of 10-13 m/s) and the engineered part of the system (namely concrete, bentonite plugs and crushed clay backfill) are expected to be more permeable with a value of 10-6 m/s for the higher (backfill). Flow and transport calculations then have to deal with highly heterogeneous multi-scale objects. In the practical calculation case, smallest objects (like canisters) are often not represented but act as source term on nodes of the computational mesh and cylindrical shape of repository cells, connecting galleries and shafts are simplified using a square section geometry. In the framework of the Euratom PAMINA project (http://www.ip-pamina.eu) we studied the error induced by those simplification by conducting comparison calculations on increasing time step and mesh refinement (leading to meshes build with millions of cells) of square section geometry and on cylindrical ones. This paper presents the results obtained.