Mayor Gary Monahan has been embroiled in a dispute with city workers after voting in favor of laying off half of Costa Mesa's workforce.
One city worker jumped to his death after getting his pink slip.
No suspects were identified in Saturday's brick throwing incident.
Police said there was a note attached, expressing dissatisfaction with the mayor.
In a statement released Sunday, the Orange County Employees Association and Costa Mesa City Employees Association denounced the vandalism incident, saying they do not condone such violent actions.
"We may have differences of opinion with Mayor Monahan, and we may have different political goals, but this is America, this is our country, and we all have the right to promote our opinions and pursue our goals without fear of this kind of inexcusable repercussion," said OCEA General Manager Nick Berardino in the statement.