The statistical problem of parameter estimation in partially observed hypoel-liptic diffusion processes is naturally occurring in many applications. However, due to the noise structure, where the noise components of the different coordinates of the multi-dimensional process operate on different time scales, standard inference tools are ill conditioned. In this paper, we propose to use a higher order scheme to discretize the process and approximate the likelihood, such that the different time scales are appropriately accounted for. We show consistency and asymptotic normality with non-typical convergence rates. When only partial observations are available, we embed the approximation into a filtering algorithm for the unobserved coordinates, and use this as a building block in a Stochastic Approximation Expectation Maximization algorithm. We illustrate on simulated data from three models; the Harmonic Oscillator, the FitzHugh-Nagumo model used to model the membrane potential evolution in neuroscience, and the Synaptic Inhibition and Excitation model used for determination of neuronal synaptic input.