THIS LINK will show you the relative frequency of the phrases.
It doesn't really answer your question though.
The trouble is, I don't think I would use either of the expressions you are asking about.
I might talk about "the test questions", or "the questions in the test", but I don't have any experience of talking about "questions in/on the test paper".
If you forced me to an answer, I would go for "questions on the test paper", but I'm not at all happy about that.