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The court for child protective services
This is the Superior Court, or, more specifically, Family Court. And, yes, a judge in the Family Court can issue an arrest warrant.
The answer to most any question that begins with, "Can a judge ...?" is most often a resounding "Yes!" Whether the ruling would stand up on appeal is a different matter. In your case, there is no way to evaluate whether an arrest warrant issued by the court might stand up to a challenge because you have provided zero details. No matter the situation, if such a warrant has been issued the defendant needs to consult an attorney immediately.