The real estate boss, according to the court, increased his salary from $200,000 to $340,000 a year and also authorised an additional "brand ambassador" payment to himself of $125,000 per annum.
Pero and another company he controls was ordered to pay back all money they received in excess of $200,000 a year.
That was later calculated as being at $2.38m once accrued interest is taken into account.
Pero and Mike Pero Mortgages cannot agree how the debt should be repaid.
Pero says that he doesn't have the ability to pay back the amount right now.
He says his only asset is his $12.5m worth of shares in Mike Pero Real Estate, which won't agree to pay out a dividend that would allow him to return the overpayment.
Pero alleged that Mike Pero Mortgages won't allow a dividend to be paid so it can acquire shares off him in the real estate business for less than they are worth.
Pero has launched separate legal action to determine whether or not a dividend should be paid and last month Justice Mary Peters agreed to put a stop on Mike Pero Mortgages' ability to enforce its debt until that matter has been resolved.
Any sale of Pero's shares in the real estate firm would reduce his interest to less than 50 per cent and the judge accepted that it may be impossible to restore it if the separate action over the dividend is successful.
On the other hand, Mike Pero Real Estate did not urgently need the $2.3m back and there was no risk of a shortfall to the company if Pero's legal fight over the dividend was unsuccessful, she said.
Justice Peters agreed to grant a stay over enforcing the debt until September this year.
