diff --git a/newsfragments/5296.bugfix.rst b/newsfragments/5296.bugfix.rst
new file mode 100644
index 0000000000..b717a3acf2
--- /dev/null
+++ b/newsfragments/5296.bugfix.rst
@@ -0,0 +1 @@
+Fixed a regression where the executable bit (and other mode bits) could be lost for ``package_data`` files that are also collected as Python modules (e.g. ``.py`` files inside PEP 420 implicit namespace subpackages), because the mode-restoring copy performed by ``build_py.build_package_data`` could be silently skipped by an ``mtime``-based "already up-to-date" check -- by :user:`agu2347`
diff --git a/setuptools/command/build_py.py b/setuptools/command/build_py.py
index 3c7c2d1bd6..48b4af2f90 100644
--- a/setuptools/command/build_py.py
+++ b/setuptools/command/build_py.py
@@ -172,6 +172,17 @@ def build_package_data(self) -> None:
         for target, srcfile in self._get_package_data_output_mapping():
             self.mkpath(os.path.dirname(target))
             _outf, _copied = self.copy_file(srcfile, target)
+            # `copy_file` may skip the actual copy (and with it, the
+            # mode-preserving chmod) if `target` already looks
+            # up-to-date based on an mtime comparison. This can happen
+            # when the same file was already staged by build_module()
+            # with preserve_mode=False, e.g. for package_data files
+            # that are also collected as Python modules (as happens
+            # with PEP 420 implicit namespace subpackages). Explicitly
+            # sync the mode bits here so package_data files always end
+            # up with the permissions of their source, regardless of
+            # whether the "up-to-date" skip kicked in. See #5296.
+            os.chmod(target, stat.S_IMODE(os.stat(srcfile).st_mode))
             make_writable(target)
 
     def analyze_manifest(self) -> None:
diff --git a/setuptools/tests/test_build_py.py b/setuptools/tests/test_build_py.py
index 62ed408f3c..5ab32bc6df 100644
--- a/setuptools/tests/test_build_py.py
+++ b/setuptools/tests/test_build_py.py
@@ -122,6 +122,47 @@ def test_executable_data(tmpdir_cwd):
     )
 
 
+@pytest.mark.xfail(
+    'platform.system() == "Windows"',
+    reason="On Windows, files do not have executable bits",
+    raises=AssertionError,
+    strict=True,
+)
+def test_executable_data_in_implicit_namespace_subpackage(tmpdir_cwd):
+    """
+    A package_data file that lives inside an implicit namespace
+    subpackage (no __init__.py) is copied twice while building:
+    once by build_module() (which discovers it as a Python module
+    and copies it with preserve_mode=False), and once by
+    build_package_data() (which should copy it with preserve_mode=True
+    to restore the correct mode). If both copies end up with
+    identical mtimes, the "up-to-date" staleness check in copy_file
+    can cause the second, mode-restoring copy to be skipped, leaving
+    the file non-executable.
+
+    Regression test for #5296.
+    """
+    dist = Distribution(
+        dict(
+            script_name='setup.py',
+            script_args=['build_py'],
+            packages=['pkg', 'pkg.scripts'],
+            package_data={'pkg': ['scripts/*']},
+        )
+    )
+    os.makedirs('pkg/scripts')
+    open('pkg/__init__.py', 'wb').close()
+    open('pkg/scripts/run-me.py', 'wb').close()
+    os.chmod('pkg/scripts/run-me.py', 0o700)
+
+    dist.parse_command_line()
+    dist.run_commands()
+
+    assert os.stat('build/lib/pkg/scripts/run-me.py').st_mode & stat.S_IEXEC, (
+        "Script is not executable"
+    )
+
+
 EXAMPLE_WITH_MANIFEST = {
     "setup.cfg": DALS(
         """