A quantum mechanical system is S indirectly controlled when the control affects an ancillary system A and the evolution of is modified through the interaction with A only. A study of indirect controllability gives a description of the set of states that can be obtained for S with this scheme. In this paper, we study the indirect controllability of quantum systems in the finite dimensional case. After discussing the relevant definitions, we give a general necessary condition for controllability in Lie algebraic terms. We present a detailed treatment of the case where both systems, S and A, are two-dimensional (qubits). In particular, we characterize the dynamical Lie algebra associated with S + A, extending previous results, and prove that complete controllability of S + A and an appropriate notion of indirect controllability are equivalent properties for this system. We also prove several further indirect controllability properties for the system of two qubits, and illustrate the role of the Lie algebraic analysis in the study of reachable states.