Queensland Police said they attended the Holland Park mosque, on the city’s south side, on Wednesday morning.
Images of the vandalism show two swastika symbols sprayed onto the mosque’s brick fence and its main sign.
A reference to an alleged right-wing mass murderer was also written, as well as “remove kebab”.
Labor MP and member for Griffith Terri Butler condemned the graffiti as "disgusting".
"Our community is vastly stronger than the anonymous coward who did this," Butler wrote on Facebook.