I've found the solution by the link http://forum.virtuemart.net/index.php?topic=127483.0 from Virtuemart Projectleader:
if (!class_exists('VirtueMartCart')) require(VMPATH_SITE . DS . 'helpers' . DS . 'cart.php');
$cart = VirtueMartCart::getCart();
$cart->removeProductCart($yourId);
but it doesn't work. I tried to replace DS with DIRECTORY_SEPARATOR because I use Joomla 3.x but nothing changed
At the same time $cart->emptyCart() works
Joomla 3.3.6, VM 3.0.3