The unsteady, compressible Navier-Stokes equations are used to compute and analyze compressible quasi-axisymmetric isolated vortices. The Navier-Stokes equations are solved using an implicit, upwind, flux difference splitting finite volume scheme. The developed three dimensional solver was verified by comparing its solution profiles with those of a slender, quasi-axisymmetric vortex solver for a subsonic, quasi-axisymmetric vortex in an unbounded domain. The Navier-Stokes solver is then used to solve for a supersonic, quasi-axisymmetric vortex flow in a configured circular duct. Steady and unsteady vortex-shock interactions and breakdown were captured. The problem was also calculated using the Euler solver of the same code; the results were compared with those of the Navier-Stokes solver. The effect of the initial swirl was investigated.