The mural appeared on a banner put up during the school's graduation ceremonies Thursday and Friday, the Bangkok Post reported.
The painting -- which has been taken down -- featured German dictator and Nazi leader Hitler along the images of Batman and Superman.
A statement from the University said the painting was "not intended to refer to anyone particularly."
Associate professor and dean of the faculty of fine and applied arts Supakorn Dispan said he spoke with the students responsible for creating the mural and determined they had no malicious intentions.
"The students only wanted to show through the mural that different superheroes are there to protect the world and that there are both good and evil people," he said. "Please do not forget that they are first year students and have been here for only a few months."
Rabbi Abraham Cooper, an official from the Simon Wiesenthal Center -- a Jewish human rights organization in the United States -- said he was "outraged and disgusted" by the university's elites' silence.
Thailand has been criticized in the past for its use of Nazi imagery. In 2011, students at a Catholic school dressed up in Nazi uniforms for a parade. Critics blame a basic lack of historical understanding for the instances, the Post said.