diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py
index eb4f6e3bf2..36be87580c 100644
--- a/lib/spack/llnl/util/filesystem.py
+++ b/lib/spack/llnl/util/filesystem.py
@@ -196,6 +196,11 @@ def change_sed_delimiter(old_delim, new_delim, *filenames):
 
 def set_install_permissions(path):
     """Set appropriate permissions on the installed file."""
+# If this points to a file maintained in a Spack prefix, it is assumed that
+# this function will be invoked on the target. If the file is outside a
+# Spack-maintained prefix, the permissions should not be modified.
+    if os.path.islink(path):
+        return
     if os.path.isdir(path):
         os.chmod(path, 0o755)
     else:
@@ -203,6 +208,10 @@ def set_install_permissions(path):
 
 
 def copy_mode(src, dest):
+    """Set the mode of dest to that of src unless it is a link.
+    """
+    if os.path.islink(dest):
+        return
     src_mode = os.stat(src).st_mode
     dest_mode = os.stat(dest).st_mode
     if src_mode & stat.S_IXUSR: