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As in the paper [G. Groenewald, M.A. Kaashoek, A.C.M. Ran, Wiener-Hopf indices of unitary functions on the unit circle in terms of realizations and related results on Toeplitz operators. \emph{Indag. Math.} 28 (2017) 694--710] our aim is to obtain explicitly the Wiener-Hopf indices of a rational $m\times m$ matrix function $R(z)$ that has no poles and no zeros on the unit circle $\mathbb{T}$ but, in contrast with that paper, the function $R(z)$ is not required to be unitary on the unit circle. On the other hand, using a Douglas-Shapiro-Shields type of factorization, we show that $R(z)$ factors as $R(z)=Ξ(z)Ψ(z)$, where $Ξ(z)$ and $Ψ(z)$ are rational $m\times m$ matrix functions, $Ξ(z)$ is unitary on the unit circle and $Ψ(z)$ is an invertible outer function. Furthermore, the fact that $Ξ(z)$ is unitary on the unit circle allows us to factor as $Ξ(z) =V(z)W^*(z)$ where $V(z)$ and $W(z)$ are rational bi-inner $m\times m$ matrix functions. The latter allows us to solve the Wiener-Hopf indices problem. To derive explicit formulas for the functions $V(z)$ and $W(z)$ requires additional realization properties of the function $Ξ(z)$ which are given in the last two sections.