Influenza A viruses (IAV) and Newcastle disease viruses (NDV) are major human and animal health threats with geographic differences in prevalence, characteristics, and host populations. Currently, there is sparse information on IAV and NDV in avian species in South Africa. Because raptors feed on live wild birds which are the reservoir hosts of IAV and NDV, we considered them a good sentinel for surveillance. Therefore, in addition to other resident birds of prey, migratory Amur falcons (Falco amurensis) were screened for IAV and NDV. Oropharyngeal and cloacal samples were collected from raptor species at three sampling sites in KwaZulu-Natal and were screened for IAV and NDV using molecular methods. IAV-positive samples were further screened for the presence of H5, H7, and H9 viruses. A total of 14 samples from 11 birds (45.8% of all sampled birds) were IAV positive with Ct lower than 36 in duplicate tests. Five out of 24 birds (20.8%) were positive for IAV RNA in duplicate testing, albeit at low concentrations. Among raptor samples, three out of 24 birds (12.5%) were positive for IAV with virus detected in both cloacal and oropharyngeal swabs. One IAV positive sample was also positive for H5 subtype (4.1%); all other samples were H5, H7, and H9 negative. Besides, all samples were NDV negative. Overall, our results support the development of more intensive and expanded influenza and other emerging virus studies in raptor species.