This paper reports on the atomic transport occurring across the interface of Cu/Ge and Co/Ge layers leading to the synthesis of Cu3Ge and Co2Ge phases under MeV Kr and Ar ion irradiations. These phases have potential applications in modern semiconductor device technology. The marker experiments show that in the case of Cu/Ge systems both Cu and Ge are mobile but Cu is the dominant moving species. On the other hand, in the case of the Co/Ge system only Ge atoms are mobile. The atomic movements during ion irradiation in these two systems have been explained on the basis of distribution of defect density and effects of thermodynamic forces.