Is it permissible to work on completing private transactions for a fee after official working hours, with the consent of the official, and does this consent override government regulations?

It appears that the officer's permission for you to use government equipment for your personal transactions violates government regulations. Therefore, it is not permissible for you to do so, and the officer's permission is of no consequence. Your actions constitute a dereliction of trust and an infringement upon it. You both must repent and not return to such actions.