We study the orbits in a Manko-Novikov type metric (MN) which is a perturbed Kerr metric. There are periodic, quasi-periodic, and chaotic orbits, which are found in configuration space and on a surface of section for various values of the energy E and the z-component of the angular momentum Lz. For relatively large Lz there are two permissible regions of non-plunging motion bounded by two closed curves of zero velocity (CZV), while in the Kerr metric there is only one closed CZV of non-plunging motion. The inner permissible region of the MN metric contains mainly chaotic orbits, but it contains also a large island of stability. We find the positions of the main periodic orbits as functions of Lz and E, and their bifurcations. Around the main periodic orbit of the outer region there are islands of stability that do not appear in the Kerr metric. In a realistic binary system, because of the gravitational radiation, the energy E and the angular momentum Lz of an inspiraling compact object decrease and therefore the orbit of the object is non-geodesic. In fact in an EMRI system the energy E and the angular momentum Lz decrease adiabatically and therefore the motion of the inspiraling object is characterized by the fundamental frequencies which are drifting slowly in time. In the Kerr metric the ratio of the fundamental frequencies changes strictly monotonically in time. However, in the MN metric when an orbit is trapped inside an island the ratio of the fundamental frequencies remains constant for some time. Hence, if such a phenomenon is observed this will indicate that the system is non integrable and therefore the central object is not a Kerr black hole.