diff --git a/reprozip/reprozip/tracer/linux_pkgs.py b/reprozip/reprozip/tracer/linux_pkgs.py
index 5ac3b7f2c..d8eeebd66 100644
--- a/reprozip/reprozip/tracer/linux_pkgs.py
+++ b/reprozip/reprozip/tracer/linux_pkgs.py
@@ -119,6 +119,14 @@ def search_for_files(self, files):
         # Remaining files are not from packages
         self.unknown_files.update(f for f in files if f.path in requested)
 
+    def _filter(self, f):
+        # Directories and non-existent files
+        if f.path.is_dir():
+            self.unknown_files.add(f)
+            return True
+
+        return super(DpkgManager, self)._filter(f)
+
     def _get_package_for_file(self, filename):
         # This method is no longer used for dpkg: instead of querying each file
         # using `dpkg -S`, we read all the list files once ourselves since it