2MeV protons and 1MeV carbon ions are bombarded on highly oriented pyrolytic graphite (HOPG) samples and their electronic transport measurements are carried out in the presence of magnetic field. The Magneto-Resistance (MR) measurements show measurable hysteresis in the resistance value after ion beam irradiation for the in-plane magnetic field direction as well as for the out-of-plane field direction. The MR depends on the thickness of the flake and the method of its separation from the bulk HOPG. The results substantiate that the ferromagnetic coupling between the magnetic moments at the vacancy defect sites in HOPG sensitively depends on the average defect separation. The average defect separation range of 1.7–0.5nm allows only a part of the 40μm thick proton beam irradiated sample to go for ferromagnetic ordering. Similar conclusions are drawn from carbon ion irradiated HOPG flake. The irradiation increases the resistance of the flake as well.