diff --git a/src/flake8/main/git.py b/src/flake8/main/git.py
index 3f9689f..096fed6 100644
--- a/src/flake8/main/git.py
+++ b/src/flake8/main/git.py
@@ -42,6 +42,7 @@ def hook(lazy=False, strict=False):
     with make_temporary_directory() as tempdir:
         filepaths = list(copy_indexed_files_to(tempdir, lazy))
         app.initialize(['.'])
+        app.options.exclude = update_excludes(app.options.exclude, tempdir)
         app.run_checks(filepaths)
 
     app.report_errors()
@@ -194,6 +195,14 @@ def config_for(parameter):
     return value.lower() in defaults.TRUTHY_VALUES
 
 
+def update_excludes(exclude_list, temporary_directory_path):
+    return [
+        (temporary_directory_path + pattern)
+        if os.path.isabs(pattern) else pattern
+        for pattern in exclude_list
+    ]
+
+
 _HOOK_TEMPLATE = """#!{executable}
 import os
 import sys