
Assuming you are in the UK, the Animal Health Trust will do DNA testing for you. Cost is £10 per sample (one per pup, plus mum, plus 2 possible Dads) - minimum cost is £50. They will tell you which, if any, pups are by the planned sire.
Sure you'll agree that this is a fairly small cost for peace of mind. Hope it works out well for you.
M.