Ge nanocrystals embedded in an amorphous SiO2 film on Si matrix were prepared by ion implantation and subsequent annealing. Neutron transmutation doping (NTD) technique was used for doping Ge nanocrystals with As impurities. The microstructure, phase and photoluminescence of NTDed Ge nanocrystals were analyzed and compared with undoped Ge nanocrystals. A new photoluminescence peak related to As impurities was found. It is discovered that impurities are expelled from larger clusters resulted from Ge nanocrystal aggregation on the sample surface. To prevent nanocrystal aggregation and assure uniform doping of As, it is necessary to adopt appropriate implantation and annealing conditions.