You could add a meta robots tag to your custom 404 page that blocks the search engines. I would not suggest that. It would be much better to fix the 404 pages then to not have the search engines index them.
Generally if a 404 page is being indexed by the search engines it is because there is link popularity pointing to it. I personally do not like to block the flow of link popularity. You could upload content and fix the page or just redirect it.