diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackedBatchRefUpdate.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackedBatchRefUpdate.java
index b328eb83e..c1f547649 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackedBatchRefUpdate.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackedBatchRefUpdate.java
@@ -179,11 +179,19 @@ class PackedBatchRefUpdate extends BatchRefUpdate {
 		Map<String, LockFile> locks = null;
 		refdb.inProcessPackedRefsLock.lock();
 		try {
-			locks = lockLooseRefs(pending);
-			if (locks == null) {
-				return;
+			PackedRefList oldPackedList;
+			if (!refdb.isInClone()) {
+				locks = lockLooseRefs(pending);
+				if (locks == null) {
+					return;
+				}
+				oldPackedList = refdb.pack(locks);
+			} else {
+				// During clone locking isn't needed since no refs exist yet.
+				// This also helps to avoid problems with refs only differing in
+				// case on a case insensitive filesystem (bug 528497)
+				oldPackedList = refdb.getPackedRefs();
 			}
-			PackedRefList oldPackedList = refdb.pack(locks);
 			RefList<Ref> newRefs = applyUpdates(walk, oldPackedList, pending);
 			if (newRefs == null) {
 				return;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
index a44acacd1..bd39e6565 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
@@ -65,6 +65,7 @@ import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.io.InterruptedIOException;
+import java.nio.file.Files;
 import java.security.DigestInputStream;
 import java.security.MessageDigest;
 import java.text.MessageFormat;
@@ -901,7 +902,7 @@ public class RefDirectory extends RefDatabase {
 		return ref;
 	}
 
-	private PackedRefList getPackedRefs() throws IOException {
+	PackedRefList getPackedRefs() throws IOException {
 		boolean trustFolderStat = getRepository().getConfig().getBoolean(
 				ConfigConstants.CONFIG_CORE_SECTION,
 				ConfigConstants.CONFIG_KEY_TRUSTFOLDERSTAT, true);
@@ -1188,6 +1189,29 @@ public class RefDirectory extends RefDatabase {
 				&& buf[4] == ' ';
 	}
 
+	/**
+	 * Detect if we are in a clone command execution
+	 *
+	 * @return {@code true} if we are currently cloning a repository
+	 * @throws IOException
+	 */
+	boolean isInClone() throws IOException {
+		return hasDanglingHead() && !packedRefsFile.exists() && !hasLooseRef();
+	}
+
+	private boolean hasDanglingHead() throws IOException {
+		Ref head = exactRef(Constants.HEAD);
+		if (head != null) {
+			ObjectId id = head.getObjectId();
+			return id == null || id.equals(ObjectId.zeroId());
+		}
+		return false;
+	}
+
+	private boolean hasLooseRef() throws IOException {
+		return Files.walk(refsDir.toPath()).anyMatch(Files::isRegularFile);
+	}
+
 	/** If the parent should fire listeners, fires them. */
 	void fireRefsChanged() {
 		final int last = lastNotifiedModCnt.get();