In this article, we consider a gauge-theoretic equation on compact symplectic 6-manifolds, which forms an elliptic system after gauge fixing. This can be thought of as a higher-dimensional analogue of the Seiberg-Witten equation. By using the virtual neighbourhood method by Ruan, we define an integer-valued invariant, a 6-dimensional Seiberg-Witten invariant, from the moduli space of solutions to the equations, assuming that the moduli space is compact; and it has no reducible solutions. We prove that the moduli spaces are compact if the underlying manifold is a compact Kahler threefold. We then compute the integers in some cases.