Acceptor-type defects in highly n-type InN are probed using positron annihilation spectroscopy. Results are compared to Hall effect measurements and calculated electron mobilities. Based on this, self-compensation in n-type InN is studied and the microscopic origin of compensating and scattering centers in irradiated and Si-doped InN is discussed. We find significant compensation through negatively charged indium vacancy complexes as well as additional acceptor-type defects with no or small effective open volume, which act as scattering centers in highly n-type InN samples.