My adviser wants to use bad statistics. Help!
Do not "change the numbers to the right ones right before I submit the paper" - this would be submitting without your co-authors approval.

If you are sure that "your" statistics are the correct ones - which sounds likely in this case - get back to your advisor with your other co-authors and the stats prof, try to convince him once more. Support your opinion with papers and/or textbooks.

Depending on how wrong your advisor's suggestion is, insist on not using it, or let it over to reviewers.