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The Morris-Shore (MS) transformation is a powerful tool for decomposition of the dynamics of multistate quantum systems to a set of two-state systems and uncoupled single states. It assumes two sets of states wherein any state in the first set can be coupled to any state in the second set but the states within each set are not coupled between themselves. Another important condition is the degeneracy of the states in each set, although all couplings between the states from different sets can be detuned from resonance by the same detuning. The degeneracy condition limits the application of the MS transformation in various physically interesting situations, e.g. in the presence of electric and/or magnetic fields or light shifts, which lift the degeneracy in each set of states, e.g. when these sets comprise the magnetic sublevels of levels with nonzero angular momentum. This paper extends the MS transformation to such situations, in which the states in each of the two sets are nondegenerate. To this end, we develop an alternative way for the derivation of Morris-Shore transformation, which can be applied to non-degenerate sets of states. We present a generalized eigenvalue approach, by which, in the limit of small detunings from degeneracy, we are able to generate an effective Hamiltonian that is dynamically equivalent to the non-degenerate Hamiltonian. The effective Hamiltonian can be mapped to the Morris-Shore basis with a two-step similarity transformation. After the derivation of the general framework, we demonstrate the application of this technique to the popular Lambda three-state system, and the four-state tripod, double-Lambda and diamond systems. In all of these systems, our formalism allows us to reduce their quantum dynamics to simpler two-state systems even in the presence of various detunings, e.g. generated by external fields of frequency drifts.