altering a hook_form_alter function
Not as such, but you can just implement your own version of that alter hook to make the changes you need to, and make sure your implementation runs later on.

To do that you'll need to implement hook_module_implements_alter():

function MYMODULE_module_implements_alter(&amp;$implementations, $hook) {
  if ($hook == 'form_alter') {
    // Push your module's implementations of hook_form_alter(), and derivatives, 
    // to last in the list. This will make it run after menu_form_node_type_form_alter()
    // so you can alter whatever you need to.
    $group = $implementations['my_module'];
    unset($implementations['my_module']);
    $implementations['my_module'] = $group;
  }
}

function MYMODULE_form_node_type_form_alter(&amp;$form, &amp;$form_state, $form_id) {
  // Make changes as usual
}