The Duo-Security people, who have an Android Token claim to use the secure element in NFC enabled phones. It is a TOTP token and can be used just like the Google Authenticator. You don't have to use Duo-Security's system to use it (though there system is worth looking at if you are rolling out your own authentication system).
URL? I don't see anything about their android "duo push" or "duo mobile" client supporting the secure element, but their website is designed around the kind of people who buy $3/mo authentication systems (enterprise, not saas developers).
