Threatening articles such as "Kill Balija (an expression used to insult Bosnian Muslims)" and "We will slaughter Muslim women and children," were written on the Franje Tudjman Bridge in Capljina, where the Croat population is concentrated.
"The murals were written by irresponsible people who aim to humiliate the Bosniak population and spread hatred, intolerance and division among the residents of Capljina. We hope that the perpetrators are found and the different institutions react." said City Administration spokesperson Danijela Nogolica.
She urged residents to be responsible to themselves and others and added the city government condemned the action and the graffiti was painted over.
Capljina police said an investigation was launched to find and punish the perpetrators.
Vandals attack a mosque last weekend in northeastern Bosnia Herzegovina that sparked backlash and widespread criticism.
The Dasnica Mosque in Bijeljina had its walls urinated on by unknown persons, according to the Islamic Union Assembly.