Upon completion of construction of the works and commencement of use of water, the permit holder shall notify the commissioner that the appropriator has perfected the appropriation. If the commissioner determines that the appropriation has been perfected in substantial accordance with the permit, the commissioner shall issue the permit holder a certificate of appropriation. The certificate shall set out any condition that the commissioner may prescribe by regulation, including conditions that are necessary to protect the prior rights of other persons and the public interest.