Inactivation of avian influenza viruses (AIVs) using chemical disinfectants is an indispensable biosecurity measure during outbreaks. The efficiency of disinfection process depends on disinfectant type and presence or absence of organic matter. It is also not clear whether AIV pathotype could influence its tolerability to a given disinfectant. Here, we assessed the efficiency of formalin and caustic soda against high (H5N1) and low (H9N2) pathogenic AIVs in the presence and absence of wet faeces. Our results showed that the effectiveness of both disinfectants depends on the target virus with the low pathogenic H9N2 virus being generally more susceptible to disinfection than the high pathogenic H5N1 virus. Wet faeces slightly influenced disinfection action in a virus- and contact time- dependent manner. This study highlights the importance of eliminating faecal matter before initiating a disinfection process and indicates the influence of disinfectant type and AIVs pathotype when selecting the appropriate disinfectant.