diff --git a/Command/Watch.hs b/Command/Watch.hs
index f9daa1a99c..d50a581a18 100644
--- a/Command/Watch.hs
+++ b/Command/Watch.hs
@@ -123,11 +123,16 @@ onAddSymlink file = go =<< Backend.lookupFile file
 {- The file could reappear at any time, so --cached is used, to only delete
  - it from the index. -}
 onDel :: FilePath -> Annex ()
-onDel file = Annex.Queue.addCommand "rm"
-	[Params "--quiet --cached --ignore-unmatch --"] [file]
+onDel file = Annex.Queue.addUpdateIndex =<<
+	inRepo (Git.UpdateIndex.unstageFile file)
 
 {- A directory has been deleted, or moved, so tell git to remove anything
- - that was inside it from its cache. -}
+ - that was inside it from its cache. Since it could reappear at any time,
+ - use --cached to only delete it from the index. 
+ -
+ - Note: This could use unstageFile, but would need to run another git
+ - command to get the recursive list of files in the directory, so rm is
+ - just as good. -}
 onDelDir :: FilePath -> Annex ()
 onDelDir dir = Annex.Queue.addCommand "rm"
 	[Params "--quiet -r --cached --ignore-unmatch --"] [dir]
diff --git a/Git/UpdateIndex.hs b/Git/UpdateIndex.hs
index faffeec667..07057ed988 100644
--- a/Git/UpdateIndex.hs
+++ b/Git/UpdateIndex.hs
@@ -13,6 +13,7 @@ module Git.UpdateIndex (
 	streamUpdateIndex,
 	lsTree,
 	updateIndexLine,
+	unstageFile,
 	stageSymlink
 ) where
 
@@ -24,6 +25,7 @@ import Git.Types
 import Git.Command
 import Git.FilePath
 import Git.HashObject
+import Git.Sha
 
 {- Streamers are passed a callback and should feed it lines in the form
  - read by update-index, and generated by ls-tree. -}
@@ -61,6 +63,12 @@ updateIndexLine :: Sha -> BlobType -> TopFilePath -> String
 updateIndexLine sha filetype file =
 	show filetype ++ " blob " ++ show sha ++ "\t" ++ getTopFilePath file
 
+{- A streamer that removes a file from the index. -}
+unstageFile :: FilePath -> Repo -> IO Streamer
+unstageFile file repo = do
+	p <- toTopFilePath file repo
+	return $ pureStreamer $ "0 " ++ show nullSha ++ "\t" ++ getTopFilePath p
+
 {- A streamer that adds a symlink to the index. -}
 stageSymlink :: FilePath -> String -> Repo -> IO Streamer
 stageSymlink file linktext repo = do