diff --git a/common/src/main/scala/org/apache/comet/CometConf.scala b/common/src/main/scala/org/apache/comet/CometConf.scala
index cccad53c53..96e4168319 100644
--- a/common/src/main/scala/org/apache/comet/CometConf.scala
+++ b/common/src/main/scala/org/apache/comet/CometConf.scala
@@ -111,6 +111,10 @@ object CometConf extends ShimCometConf {
       .booleanConf
       .createWithDefault(false)
 
+  // Deprecated: native_comet uses mutable buffers incompatible with Arrow FFI best practices
+  // and does not support complex types. Use native_iceberg_compat or auto instead.
+  // See: https://github.com/apache/datafusion-comet/issues/2186
+  @deprecated("Use SCAN_AUTO instead", "0.9.0")
   val SCAN_NATIVE_COMET = "native_comet"
   val SCAN_NATIVE_DATAFUSION = "native_datafusion"
   val SCAN_NATIVE_ICEBERG_COMPAT = "native_iceberg_compat"
@@ -121,11 +125,11 @@ object CometConf extends ShimCometConf {
     .doc(
       s"The implementation of Comet Native Scan to use. Available modes are `$SCAN_NATIVE_COMET`," +
         s"`$SCAN_NATIVE_DATAFUSION`, and `$SCAN_NATIVE_ICEBERG_COMPAT`. " +
-        s"`$SCAN_NATIVE_COMET` is for the original Comet native scan which uses a jvm based " +
-        "parquet file reader and native column decoding. Supports simple types only " +
-        s"`$SCAN_NATIVE_DATAFUSION` is a fully native implementation of scan based on DataFusion" +
-        s"`$SCAN_NATIVE_ICEBERG_COMPAT` is a native implementation that exposes apis to read " +
-        s"parquet columns natively. `$SCAN_AUTO` chooses the best scan.")
+        s"`$SCAN_NATIVE_COMET` (DEPRECATED) is for the original Comet native scan which uses a jvm based " +
+        "parquet file reader and native column decoding. Supports simple types only. " +
+        s"`$SCAN_NATIVE_DATAFUSION` is a fully native implementation of scan based on DataFusion. " +
+        s"`$SCAN_NATIVE_ICEBERG_COMPAT` is the recommended native implementation that exposes apis to read " +
+        s"parquet columns natively and supports complex types. `$SCAN_AUTO` (default) chooses the best scan.")
     .internal()
     .stringConf
     .transform(_.toLowerCase(Locale.ROOT))