The conversion of whey permeates to galacto-oligosaccharides (GOS) was studied by the enzymatic action of β-galactosidase from Aspergillus oryzae in a continuous flow packed-bed reactor. A novel method of enzyme immobilization involving covalent immobilization of β-galactosidase on 3-aminopropyl triethoxysilane(3-APTES)-modified glass beads was developed by the cross-linking method. The pH and temperature dependence of the enzymatic efficiency of the glass bead-immobilized enzyme was compared with that of the free enzyme. Increased pH and thermal stabilities were observed for the immobilized enzyme versus the free enzyme. The reusability of the enzyme immobilized packed-bed reactor was studied and only about 4.6% of GOS yield was lost after eight reuses. Repeated cycle reactions were also carried out to improve the formation of GOS. The results showed that the GOS formation increased and a maximum GOS yield of 39.3% with 56.4% lactose conversion was obtained after the 2nd cycle of passing.