Unless you have a contract which states that you will pay ESCT on top of you employer contributions, then you do not need to.
Your employee is receiving less in their KiwiSaver account because of the ESCT deduction, but there is no obligation for you to take on an additional cost to make up for it. You are still contributing the amount required, and complying with your obligations.
A superannuation contribution must be at least 3% of the employee’s salary or wages.