Comal County Judge Sherman Krause broke the news to the New Braunfels ISD school board at a special meeting Wednesday.
He said the long-vacant Scooter Store headquarters is off the table as a possible site for the Comal County Justice Center.
Krause said the decision actually was reached last week based primarily on the estimated $30 million cost.
He said voters already had rejected a similar proposal a few years ago.
Superintendent Randy Moczygemba said he was surprised by the county's decision, which was announced minutes before the board took up a resolution opposing the idea.
Moczygemba said he was concerned about the Scooter Store's proximity to a high school, middle school and two of three elementary schools planned behind the site along Loop 337.
He said he was worried about a possible incident involving the public, not inmates under guard.
As for what to do with the landlocked courthouse downtown, the county judge said the options are undecided.
But Krause said the commissioners court may look at expanding the Comal County Jail.