The effects of variations in net toroidal current on the Mercier criterion are studied in a heliotron configuration under the free boundary condition. The plasma column and the magnetic axis are shifted horizontally by the net toroidal current because the free boundary condition changes the effective vertical field. The direction of the shift depends on the direction of the current. In the case of a subtractive current density peaked at the axis, which decreases the rotational transform, the equilibrium is more stable than the no net current equilibrium, although the plasma axis is shifted inwards by the current itself. This is because the Shafranov shift is greater than the inward axis shift caused by the current itself, and the magnetic well is enhanced. In the case of additive currents which increase the rotational transform, there is a tendency for the stability to be improved as the peak position of the current density varies from the axis to the peripheral region. This improvement is due to the enhancement of the magnetic shear at low beta and the magnetic well at high beta. As in the no net current case, the equilibrium with an additive hollow current under the free boundary condition is more stable than that under the fixed boundary condition because magnetic well stabilization is enhanced. When the subtractive current peaked at the axis and the additive hollow current flow simultaneously so that the total current is zero or slightly additive, the interchange mode can be stabilized even if the corresponding equilibrium with no net current is strongly Mercier unstable.