diff --git a/lib/storage/partition.go b/lib/storage/partition.go
index 5ee2cc1e6..d7af8a17a 100644
--- a/lib/storage/partition.go
+++ b/lib/storage/partition.go
@@ -1394,17 +1394,14 @@ func (pt *partition) removeStaleParts() {
 	}
 
 	// Physically remove stale parts under snapshotLock in order to provide
-	// consistent snapshots with partition.CreateSnapshot().
+	// consistent snapshots with table.CreateSnapshot().
 	pt.snapshotLock.RLock()
-	var removeWG sync.WaitGroup
 	for pw := range m {
 		logger.Infof("removing part %q, since its data is out of the configured retention (%d secs)", pw.p.path, pt.retentionMsecs/1000)
-		removeWG.Add(1)
-		fs.MustRemoveAllWithDoneCallback(pw.p.path, removeWG.Done)
+		fs.MustRemoveDirAtomic(pw.p.path)
 	}
-	removeWG.Wait()
 	// There is no need in calling fs.MustSyncPath() on pt.smallPartsPath and pt.bigPartsPath,
-	// since they should be automatically called inside fs.MustRemoveAllWithDoneCallback.
+	// since they should be automatically called inside fs.MustRemoveDirAtomic().
 
 	pt.snapshotLock.RUnlock()
 
@@ -1554,6 +1551,7 @@ func openParts(pathPrefix1, pathPrefix2, path string) ([]*partWrapper, error) {
 	if err := fs.MkdirAllIfNotExist(path); err != nil {
 		return nil, err
 	}
+	fs.MustRemoveTemporaryDirs(path)
 	d, err := os.Open(path)
 	if err != nil {
 		return nil, fmt.Errorf("cannot open directory %q: %w", path, err)
@@ -1568,9 +1566,9 @@ func openParts(pathPrefix1, pathPrefix2, path string) ([]*partWrapper, error) {
 	}
 
 	txnDir := path + "/txn"
-	fs.MustRemoveAll(txnDir)
+	fs.MustRemoveDirAtomic(txnDir)
 	tmpDir := path + "/tmp"
-	fs.MustRemoveAll(tmpDir)
+	fs.MustRemoveDirAtomic(tmpDir)
 	if err := createPartitionDirs(path); err != nil {
 		return nil, fmt.Errorf("cannot create directories for partition %q: %w", path, err)
 	}
@@ -1596,7 +1594,7 @@ func openParts(pathPrefix1, pathPrefix2, path string) ([]*partWrapper, error) {
 		if fs.IsEmptyDir(partPath) {
 			// Remove empty directory, which can be left after unclean shutdown on NFS.
 			// See https://github.com/VictoriaMetrics/VictoriaMetrics/issues/1142
-			fs.MustRemoveAll(partPath)
+			fs.MustRemoveDirAtomic(partPath)
 			continue
 		}
 		startTime := time.Now()
@@ -1761,14 +1759,12 @@ func runTransaction(txnLock *sync.RWMutex, pathPrefix1, pathPrefix2, txnPath str
 	}
 
 	// Remove old paths. It is OK if certain paths don't exist.
-	var removeWG sync.WaitGroup
 	for _, path := range rmPaths {
 		path, err := validatePath(pathPrefix1, pathPrefix2, path)
 		if err != nil {
 			return fmt.Errorf("invalid path to remove: %w", err)
 		}
-		removeWG.Add(1)
-		fs.MustRemoveAllWithDoneCallback(path, removeWG.Done)
+		fs.MustRemoveDirAtomic(path)
 	}
 
 	// Move the new part to new directory.
@@ -1797,8 +1793,7 @@ func runTransaction(txnLock *sync.RWMutex, pathPrefix1, pathPrefix2, txnPath str
 		}
 	} else {
 		// Just remove srcPath.
-		removeWG.Add(1)
-		fs.MustRemoveAllWithDoneCallback(srcPath, removeWG.Done)
+		fs.MustRemoveDirAtomic(srcPath)
 	}
 
 	// Flush pathPrefix* directory metadata to the underying storage,
@@ -1809,12 +1804,9 @@ func runTransaction(txnLock *sync.RWMutex, pathPrefix1, pathPrefix2, txnPath str
 	pendingTxnDeletionsWG.Add(1)
 	go func() {
 		defer pendingTxnDeletionsWG.Done()
-		// Remove the transaction file only after all the source paths are deleted.
-		// This is required for NFS mounts. See https://github.com/VictoriaMetrics/VictoriaMetrics/issues/61 .
-		removeWG.Wait()
 
 		// There is no need in calling fs.MustSyncPath for pathPrefix* after parts' removal,
-		// since it is already called by fs.MustRemoveAllWithDoneCallback.
+		// since it is already called by fs.MustRemoveDirAtomic.
 
 		if err := os.Remove(txnPath); err != nil {
 			logger.Errorf("cannot remove transaction file %q: %s", txnPath, err)