diff --git a/gradle/java/core-mrjar.gradle b/gradle/java/core-mrjar.gradle
index 40ba769c9692..0870ebdbcad3 100644
--- a/gradle/java/core-mrjar.gradle
+++ b/gradle/java/core-mrjar.gradle
@@ -46,15 +46,22 @@ configure(project(":lucene:core")) {
     }
     
     tasks.named('jar').configure {
+      boolean needMRJAR = false;
       mrjarJavaVersions.each { jdkVersion ->
-        into("META-INF/versions/${jdkVersion}") {
+        // the sourceSet which corresponds to the mininum/base Java version
+        // will copy its output to root of JAR, all other sourceSets will go into MR-JAR folders:
+        boolean isBaseVersion = (jdkVersion.toString() == rootProject.minJavaVersion.toString())
+        into(isBaseVersion ? '' : "META-INF/versions/${jdkVersion}") {
           from sourceSets["main${jdkVersion}"].output
         }
+        needMRJAR |= !isBaseVersion
       }
 
-      manifest.attributes(
-        'Multi-Release': 'true'
-      )
+      if (needMRJAR) {
+        manifest.attributes(
+          'Multi-Release': 'true'
+        )
+      }
     }
   }
 }
diff --git a/lucene/CHANGES.txt b/lucene/CHANGES.txt
index 9a4883b10533..b1061599876d 100644
--- a/lucene/CHANGES.txt
+++ b/lucene/CHANGES.txt
@@ -84,8 +84,8 @@ API Changes
   make compile() only return the FSTMetadata. For on-heap (default) use case, please use
   FST.fromFSTReader(fstMetadata, fstCompiler.getFSTReader()) to create the FST. (Anh Dung Bui)
 
-* GITHUB#13146: Remove ByteBufferIndexInput and only use MemorySegment APIs for MMapDirectory.
-  (Uwe Schindler)
+* GITHUB#13146, GITHUB#13148: Remove ByteBufferIndexInput and only use MemorySegment APIs
+  for MMapDirectory.  (Uwe Schindler)
 
 New Features
 ---------------------
diff --git a/lucene/distribution.tests/src/test/org/apache/lucene/distribution/TestModularLayer.java b/lucene/distribution.tests/src/test/org/apache/lucene/distribution/TestModularLayer.java
index 084a044092f6..84d5df2256aa 100644
--- a/lucene/distribution.tests/src/test/org/apache/lucene/distribution/TestModularLayer.java
+++ b/lucene/distribution.tests/src/test/org/apache/lucene/distribution/TestModularLayer.java
@@ -207,16 +207,25 @@ public void testMultiReleaseJar() {
 
               ClassLoader loader = layer.findLoader(coreModuleId);
 
-              final Set<Integer> jarVersions = Set.of(21);
-              for (var v : jarVersions) {
-                Assertions.assertThat(
-                        loader.getResource(
-                            "META-INF/versions/"
-                                + v
-                                + "/org/apache/lucene/store/MemorySegmentIndexInput.class"))
-                    .isNotNull();
-              }
-
+              final Set<Integer> mrJarVersions = Set.of(21);
+              final Integer baseVersion = 21;
+
+              // the Java 21 PanamaVectorizationProvider must always be in main section of JAR file:
+              final String panamaClassName =
+                  "org/apache/lucene/internal/vectorization/PanamaVectorizationProvider.class";
+              Assertions.assertThat(loader.getResource(panamaClassName)).isNotNull();
+
+              // additional versions must be in MR-JAR part
+              mrJarVersions.stream()
+                  .filter(Predicate.not(baseVersion::equals))
+                  .forEach(
+                      v -> {
+                        Assertions.assertThat(
+                                loader.getResource("META-INF/versions/" + v + panamaClassName))
+                            .isNotNull();
+                      });
+
+              // you must be always able to load MemorySegmentIndexInput:
               Assertions.assertThat(
                       loader.loadClass("org.apache.lucene.store.MemorySegmentIndexInput"))
                   .isNotNull();