in case you did not read the javacards specs yet: it is simply not possible, even if you cry. Yup.
Native methods for javacards cannot be written by javacard users, only by the Card OS manufacturer.
It is not possible unless the Java Card platform provides some proprietary break-out ability.
Some cards may offer you such capabilities, but most of the time it won't be easy to access them directly. If they do they may be constrained, or you may need additional keys, sign an NDA etc. If you are big or interesting enough of course, doors that are closed to others may open. Beware though that altering the system in such a way may seriously complicate certification of the product, especially for the OS manufacturer.
NXP JCOP cards may offer native capability, but the API is relatively low level and sandboxed.