Alter views 'Has taxonomy term' filter Programatically using views_get_view
I managed to achieve this using the following

$view = views_get_view('list_control');
$view-&gt;set_display('block_1');
$view-&gt;set_arguments(array($current_node)); // Remove current NID
$view-&gt;set_items_per_page($pager_count); // Set pager Items

// Set filter based on $tags.
$filter = $view-&gt;get_item($display_id, 'filter', 'tid');
$filter['value'] =  $tags;    
$view-&gt;set_item($display_id, 'filter', 'tid', $filter);
$view-&gt;pre_execute();
$view-&gt;execute();