How to remove a menu path defined in hook_menu from naviagtion
Don't add type to the array in hook_menu, it will not be displayed as a menu, but still will be accessible (by code)

$items['menu/%/link1'] = array(
   'title' =&gt; 'Link1',
// 'type' =&gt; MENU_LOCAL_TASK,
   'page callback' =&gt; 'link1()',
   'page arguments' =&gt; array(1),
   'access callback' =&gt; TRUE, //'has_access',
);