diff --git a/pkg/snapshot/layered_map.go b/pkg/snapshot/layered_map.go
index 976ad19d1..60e802b7b 100644
--- a/pkg/snapshot/layered_map.go
+++ b/pkg/snapshot/layered_map.go
@@ -26,6 +26,7 @@ import (
 
 	"github.com/GoogleContainerTools/kaniko/pkg/timing"
 	"github.com/GoogleContainerTools/kaniko/pkg/util"
+	"github.com/docker/docker/pkg/archive"
 	"github.com/sirupsen/logrus"
 )
 
@@ -61,15 +62,18 @@ func (l *LayeredMap) Key() (string, error) {
 	return util.SHA256(c)
 }
 
-// GetFlattenedPathsForWhiteOut returns all paths in the current FS
-func (l *LayeredMap) getFlattenedPathsForWhiteOut() map[string]struct{} {
+// getFlattenedPaths returns all existing paths in the current FS
+func (l *LayeredMap) getFlattenedPaths() map[string]struct{} {
 	paths := map[string]struct{}{}
 	for _, l := range l.layers {
 		for p := range l {
-			if strings.HasPrefix(filepath.Base(p), ".wh.") {
-				delete(paths, p)
+			basename := filepath.Base(p)
+			if strings.HasPrefix(basename, archive.WhiteoutPrefix) {
+				deletedFile := filepath.Join(filepath.Dir(p), strings.TrimPrefix(basename, archive.WhiteoutPrefix))
+				delete(paths, deletedFile)
+			} else {
+				paths[p] = struct{}{}
 			}
-			paths[p] = struct{}{}
 		}
 	}
 	return paths
diff --git a/pkg/snapshot/snapshot.go b/pkg/snapshot/snapshot.go
index ba7371846..50fa803a0 100644
--- a/pkg/snapshot/snapshot.go
+++ b/pkg/snapshot/snapshot.go
@@ -93,7 +93,7 @@ func (s *Snapshotter) TakeSnapshot(files []string, shdCheckDelete bool, forceBui
 	// Get whiteout paths
 	filesToWhiteout := []string{}
 	if shdCheckDelete {
-		_, deletedFiles := util.WalkFS(s.directory, s.l.getFlattenedPathsForWhiteOut(), func(s string) (bool, error) {
+		_, deletedFiles := util.WalkFS(s.directory, s.l.getFlattenedPaths(), func(s string) (bool, error) {
 			return true, nil
 		})
 		// The paths left here are the ones that have been deleted in this layer.
@@ -159,7 +159,7 @@ func (s *Snapshotter) scanFullFilesystem() ([]string, []string, error) {
 
 	s.l.Snapshot()
 
-	changedPaths, deletedPaths := util.WalkFS(s.directory, s.l.getFlattenedPathsForWhiteOut(), s.l.CheckFileChange)
+	changedPaths, deletedPaths := util.WalkFS(s.directory, s.l.getFlattenedPaths(), s.l.CheckFileChange)
 	timer := timing.Start("Resolving Paths")
 
 	filesToAdd := []string{}