diff --git a/build-tools-internal/src/integTest/groovy/org/elasticsearch/gradle/internal/transport/TransportVersionManagementPluginFuncTest.groovy b/build-tools-internal/src/integTest/groovy/org/elasticsearch/gradle/internal/transport/TransportVersionManagementPluginFuncTest.groovy
index 18df5a99260cb..f74639bf7d841 100644
--- a/build-tools-internal/src/integTest/groovy/org/elasticsearch/gradle/internal/transport/TransportVersionManagementPluginFuncTest.groovy
+++ b/build-tools-internal/src/integTest/groovy/org/elasticsearch/gradle/internal/transport/TransportVersionManagementPluginFuncTest.groovy
@@ -46,8 +46,8 @@ class TransportVersionManagementPluginFuncTest extends AbstractGradleFuncTest {
         javaResource("myserver", "transport/definitions/named/" + name + ".csv", ids)
     }
 
-    def initialTransportVersion(String name, String id) {
-        javaResource("myserver", "transport/definitions/initial/" + name + ".csv", id)
+    def unreferencedTransportVersion(String name, String id) {
+        javaResource("myserver", "transport/definitions/unreferenced/" + name + ".csv", id)
     }
 
     def definedAndUsedTransportVersion(String name, String ids) {
@@ -101,7 +101,7 @@ class TransportVersionManagementPluginFuncTest extends AbstractGradleFuncTest {
         """
         namedTransportVersion("existing_91", "8012000")
         namedTransportVersion("existing_92", "8123000,8012001")
-        initialTransportVersion("initial_9_0_0", "8000000")
+        unreferencedTransportVersion("initial_9_0_0", "8000000")
         latestTransportVersion("9.2", "existing_92", "8123000")
         latestTransportVersion("9.1", "existing_92", "8012001")
         // a mock version of TransportVersion, just here so we can compile Dummy.java et al
@@ -303,4 +303,14 @@ class TransportVersionManagementPluginFuncTest extends AbstractGradleFuncTest {
         assertDefinitionsFailure(result, "Transport version definition file " +
             "[myserver/src/main/resources/transport/definitions/named/patch.csv] has patch version 8015001 as primary id")
     }
+
+    def "unreferenced directory is optional"() {
+        given:
+        file("myserver/src/main/resources/transport/unreferenced/initial_9_0_0.csv").delete()
+        file("myserver/src/main/resources/transport/unreferenced").deleteDir()
+        when:
+        def result = gradleRunner(":myserver:validateTransportVersionDefinitions").build()
+        then:
+        result.task(":myserver:validateTransportVersionDefinitions").outcome == TaskOutcome.SUCCESS
+    }
 }
diff --git a/build-tools-internal/src/main/java/org/elasticsearch/gradle/internal/transport/ValidateTransportVersionResourcesTask.java b/build-tools-internal/src/main/java/org/elasticsearch/gradle/internal/transport/ValidateTransportVersionResourcesTask.java
index e23dce8f05fce..915aca66b421f 100644
--- a/build-tools-internal/src/main/java/org/elasticsearch/gradle/internal/transport/ValidateTransportVersionResourcesTask.java
+++ b/build-tools-internal/src/main/java/org/elasticsearch/gradle/internal/transport/ValidateTransportVersionResourcesTask.java
@@ -110,10 +110,13 @@ public void validateTransportVersions() throws IOException {
         // now load all definitions, do some validation and record them by various keys for later quick lookup
         // NOTE: this must run after loading referenced names and existing definitions
         // NOTE: this is sorted so that the order of cross validation is deterministic
-        for (String subDir : List.of("initial", "named")) {
-            try (var definitionsStream = Files.list(definitionsDir.resolve(subDir)).sorted()) {
-                for (var definitionFile : definitionsStream.toList()) {
-                    recordAndValidateDefinition(readDefinitionFile(definitionFile));
+        for (String subDirName : List.of("unreferenced", "named")) {
+            Path subDir = definitionsDir.resolve(subDirName);
+            if (Files.isDirectory(subDir)) {
+                try (var definitionsStream = Files.list(subDir).sorted()) {
+                    for (var definitionFile : definitionsStream.toList()) {
+                        recordAndValidateDefinition(readDefinitionFile(definitionFile));
+                    }
                 }
             }
         }
diff --git a/server/src/main/resources/transport/definitions/initial/initial_elasticsearch_8_18_5.csv b/server/src/main/resources/transport/definitions/unreferenced/initial_elasticsearch_8_18_5.csv
similarity index 100%
rename from server/src/main/resources/transport/definitions/initial/initial_elasticsearch_8_18_5.csv
rename to server/src/main/resources/transport/definitions/unreferenced/initial_elasticsearch_8_18_5.csv
diff --git a/server/src/main/resources/transport/definitions/initial/initial_elasticsearch_9_0_5.csv b/server/src/main/resources/transport/definitions/unreferenced/initial_elasticsearch_9_0_5.csv
similarity index 100%
rename from server/src/main/resources/transport/definitions/initial/initial_elasticsearch_9_0_5.csv
rename to server/src/main/resources/transport/definitions/unreferenced/initial_elasticsearch_9_0_5.csv