/**
 * Implements hook_views_pre_render().
 */
function MYMODULE_views_pre_render(&$view) {
  global $user;

  // Iterate over View results for our custom entity
  if ($view->base_table == 'my_entity_base_table') {
    foreach ($view->result as $index => $row) {

      // Presuming eid is the entity PK
      $results = entity_load('my_entity_machine_name', array($row->eid));
      if (!empty($results)) {
        $entity = $results[$row->eid];

        // If the custom access callback returns FALSE, remove from results.
        if (!my_entity_access_callback('view', $entity, $user)) {
          unset($view->result[$index]);
        }
      }
    }
  }
}