Salmonid alphavirus 3 (SAV3) causes pancreas disease (PD), which is a major problem in Norwegian aquaculture of Atlantic salmon. In this work we studied antiviral activities of salmon type I interferons IFNa, IFNb and IFNc against SAV3 infection in cell culture and in live fish to increase the understanding of the innate immunity of salmon against this virus. Recombinant IFNa, IFNb and IFNc all induced antiviral activity against SAV3 in ASK cells. For in vivo studies, we injected salmon presmolts intramuscularly with plasmids encoding salmon IFNa, IFNb and IFNc or a control plasmid and measured expression of the antiviral protein Mx in pancreas after 2 and 10 weeks and protection against SAV3 infection after 10 weeks. IFNb and IFNc plasmids, but not IFNa plasmid induced Mx expression in pancreas as shown by RT-qPCR and immunohistochemistry. A high level of protection against SAV3 infection by IFNc plasmid was observed by a strong reduction of virus load in serum and by a marked reduction in pathology of pancreas and heart compared to control fish. Lesser but significant protection was observed with IFNb plasmid while no protection was observed after treatment with IFNa plasmid. Taken together, this work suggests that IFNa provides protection of salmon against SAV3 locally in an infected area while IFNb and IFNc provides systemic protection against the virus.