Transport-related problem behaviors (TRPBs) in horses are an animal welfare concern, and many training methods in loading/travelling have been recommended to reduce their incidence. This study aimed to investigate the incidence of TRPB and training methods in Australia and to identify risks for and consequences of TRPB. An online survey was conducted, and respondents reported whether and how they trained horses for loading and/or travelling. They were also asked whether their horses suffered from transport-related problem behaviors or injuries, the industry sector in which they participated and details of the vehicle used for transport. TRPB were classified into preloading, loading, travelling (TPB), and unloading. Training methods were classified into operant conditioning (OC), self-loading (SL), habituation (H), and no training (NT). TRPB were reported by 38.0% of respondents, mainly at loading and travelling. Although 43.5% of respondents did not train their horses, OC, H, and SL were applied by 25.5%, 20.2%, and 10.8%, respectively. In 98% of cases, OC was applied by negative reinforcement/positive punishment. Training method was identified as a risk factor for all types of TRPB: their odds were higher in horses trained by OC and NT compared to SL and H. Racing horses were at high risk of TPB (P < .001). Two-horse straight float was associated with a higher risk of preloading (P = .018) and loading problem behaviors (P = .007) and injuries (P = .022). While loading and travelling problems were a risk factor for transport-related injuries, H and SL reduced this risk. These training approaches are recommended to safeguard horse welfare during transport.