diff --git a/src/java/org/apache/lucene/index/IndexWriter.java b/src/java/org/apache/lucene/index/IndexWriter.java
index fa1335c12cf..41e2a6d3bd1 100644
--- a/src/java/org/apache/lucene/index/IndexWriter.java
+++ b/src/java/org/apache/lucene/index/IndexWriter.java
@@ -206,7 +206,8 @@ public final class IndexWriter {
     flushRamSegments();
     while (segmentInfos.size() > 1 ||
 	   (segmentInfos.size() == 1 &&
-	    SegmentReader.hasDeletions(segmentInfos.info(0)))){
+	    (SegmentReader.hasDeletions(segmentInfos.info(0)) ||
+             segmentInfos.info(0).dir != directory))) {
       int minSegment = segmentInfos.size() - mergeFactor;
       mergeSegments(minSegment < 0 ? 0 : minSegment);
     }