diff --git a/internal/datacoord/meta.go b/internal/datacoord/meta.go
index 1b536c6295..8375043787 100644
--- a/internal/datacoord/meta.go
+++ b/internal/datacoord/meta.go
@@ -865,7 +865,7 @@ func (m *meta) CompleteMergeCompaction(compactionLogs []*datapb.CompactionSegmen
 	}
 
 	for _, s := range segments {
-		m.segments.DropSegment(s.GetID())
+		m.segments.SetSegment(s.GetID(), s)
 	}
 
 	// Handle empty segment generated by merge-compaction
diff --git a/internal/rootcoord/root_coord.go b/internal/rootcoord/root_coord.go
index ebec2e1f2e..dab6e7506f 100644
--- a/internal/rootcoord/root_coord.go
+++ b/internal/rootcoord/root_coord.go
@@ -902,7 +902,7 @@ func (c *Core) SetIndexCoord(s types.IndexCoord) error {
 	c.CallRemoveIndexService = func(ctx context.Context, buildIDs []UniqueID) (retErr error) {
 		defer func() {
 			if err := recover(); err != nil {
-				retErr = fmt.Errorf("get index state from index service panic, msg = %v", err)
+				retErr = fmt.Errorf("remove index from index service panic, msg = %v", err)
 			}
 		}()
 		<-initCh
@@ -2242,7 +2242,7 @@ func (c *Core) InvalidateCollectionMetaCache(ctx context.Context, in *proxypb.In
 }
 
 // SegmentFlushCompleted check whether segment flush has completed
-func (c *Core) SegmentFlushCompleted(ctx context.Context, in *datapb.SegmentFlushCompletedMsg) (*commonpb.Status, error) {
+func (c *Core) SegmentFlushCompleted(ctx context.Context, in *datapb.SegmentFlushCompletedMsg) (status *commonpb.Status, err error) {
 	if code, ok := c.checkHealthy(); !ok {
 		return failStatus(commonpb.ErrorCode_UnexpectedError, "StateCode="+internalpb.StateCode_name[int32(code)]), nil
 	}
@@ -2252,7 +2252,23 @@ func (c *Core) SegmentFlushCompleted(ctx context.Context, in *datapb.SegmentFlus
 
 	log.Info("SegmentFlushCompleted received", zap.Int64("msgID", in.Base.MsgID), zap.Int64("collID", in.Segment.CollectionID),
 		zap.Int64("partID", in.Segment.PartitionID), zap.Int64("segID", in.Segment.ID), zap.Int64s("compactFrom", in.Segment.CompactionFrom))
-	err := c.createIndexForSegment(ctx, in.Segment.CollectionID, in.Segment.PartitionID, in.Segment.ID, in.Segment.NumOfRows, in.Segment.Binlogs)
+	// acquire reference lock before building index
+	if in.Segment.CreatedByCompaction {
+		log.Debug("try to acquire segment reference lock", zap.Int64("task id", in.Base.MsgID), zap.Int64s("segmentIDs", in.Segment.CompactionFrom))
+		if err := c.CallAddSegRefLock(ctx, in.Base.MsgID, in.Segment.CompactionFrom); err != nil {
+			log.Warn("acquire segment reference lock failed", zap.Int64("task id", in.Base.MsgID), zap.Int64s("segmentIDs", in.Segment.CompactionFrom))
+			return failStatus(commonpb.ErrorCode_UnexpectedError, "AcquireSegRefLock failed: "+err.Error()), nil
+		}
+		defer func() {
+			if err := c.CallReleaseSegRefLock(ctx, in.Base.MsgID, in.Segment.CompactionFrom); err != nil {
+				log.Warn("release segment reference lock failed", zap.Int64("task id", in.Base.MsgID), zap.Int64s("segmentIDs", in.Segment.CompactionFrom))
+				// panic to let ref manager detect release failure
+				panic(err)
+			}
+		}()
+	}
+
+	err = c.createIndexForSegment(ctx, in.Segment.CollectionID, in.Segment.PartitionID, in.Segment.ID, in.Segment.NumOfRows, in.Segment.Binlogs)
 	if err != nil {
 		log.Error("createIndexForSegment", zap.Int64("msgID", in.Base.MsgID), zap.Int64("collID", in.Segment.CollectionID),
 			zap.Int64("partID", in.Segment.PartitionID), zap.Int64("segID", in.Segment.ID), zap.Error(err))
@@ -2275,6 +2291,7 @@ func (c *Core) SegmentFlushCompleted(ctx context.Context, in *datapb.SegmentFlus
 			zap.Int64s("compactFrom", in.Segment.CompactionFrom), zap.Error(err))
 		return failStatus(commonpb.ErrorCode_UnexpectedError, err.Error()), nil
 	}
+
 	log.Debug("SegmentFlushCompleted success", zap.String("role", typeutil.RootCoordRole),
 		zap.Int64("collection id", in.Segment.CollectionID), zap.Int64("partition id", in.Segment.PartitionID),
 		zap.Int64("segment id", in.Segment.ID), zap.Int64("msgID", in.Base.MsgID))
diff --git a/internal/rootcoord/root_coord_test.go b/internal/rootcoord/root_coord_test.go
index 5594aab23b..5dec5b02f0 100644
--- a/internal/rootcoord/root_coord_test.go
+++ b/internal/rootcoord/root_coord_test.go
@@ -381,6 +381,15 @@ func (idx *indexMock) DropIndex(ctx context.Context, req *indexpb.DropIndexReque
 	}, nil
 }
 
+func (idx *indexMock) RemoveIndex(ctx context.Context, req *indexpb.RemoveIndexRequest) (*commonpb.Status, error) {
+	idx.mutex.Lock()
+	defer idx.mutex.Unlock()
+	return &commonpb.Status{
+		ErrorCode: commonpb.ErrorCode_Success,
+		Reason:    "",
+	}, nil
+}
+
 func (idx *indexMock) getFileArray() []string {
 	idx.mutex.Lock()
 	defer idx.mutex.Unlock()
@@ -1443,6 +1452,46 @@ func TestRootCoord_Base(t *testing.T) {
 		assert.Equal(t, Params.CommonCfg.DefaultIndexName, rsp.IndexDescriptions[0].IndexName)
 	})
 
+	t.Run("flush segment from compaction", func(t *testing.T) {
+		coll, err := core.MetaTable.GetCollectionByName(collName, 0)
+		assert.NoError(t, err)
+		partID := coll.PartitionIDs[1]
+
+		flushMsg := datapb.SegmentFlushCompletedMsg{
+			Base: &commonpb.MsgBase{
+				MsgType: commonpb.MsgType_SegmentFlushDone,
+			},
+			Segment: &datapb.SegmentInfo{
+				ID:                  segID + 1,
+				CollectionID:        coll.ID,
+				PartitionID:         partID,
+				CompactionFrom:      []int64{segID},
+				CreatedByCompaction: true,
+			},
+		}
+		st, err := core.SegmentFlushCompleted(ctx, &flushMsg)
+		assert.NoError(t, err)
+		assert.Equal(t, st.ErrorCode, commonpb.ErrorCode_Success)
+
+		req := &milvuspb.DescribeIndexRequest{
+			Base: &commonpb.MsgBase{
+				MsgType:   commonpb.MsgType_DescribeIndex,
+				MsgID:     210,
+				Timestamp: 210,
+				SourceID:  210,
+			},
+			DbName:         "",
+			CollectionName: collName,
+			FieldName:      "vector",
+			IndexName:      "",
+		}
+		rsp, err := core.DescribeIndex(ctx, req)
+		assert.NoError(t, err)
+		assert.Equal(t, commonpb.ErrorCode_Success, rsp.Status.ErrorCode)
+		assert.Equal(t, 1, len(rsp.IndexDescriptions))
+		assert.Equal(t, Params.CommonCfg.DefaultIndexName, rsp.IndexDescriptions[0].IndexName)
+	})
+
 	wg.Add(1)
 	t.Run("import", func(t *testing.T) {
 		defer wg.Done()