Let $(B,\Delta,\mathscr{A})$ be a compact simple integral affine 3-manifold with singularities without negative vertices. Then there is a compact smooth symplectic 6-manifold $(X,\omega)$ and a $C^{\infty}$ Lagrangian fibration $f:X\rightarrow B$ with discriminant locus $\Delta$, which is a semi-stable compactification of the $T^{3}$ bundle $X(B_{0},\mathscr{A})\rightarrow B_{0}$.