In an open letter to the university, Auditor-General John Ryan said that Joyce's consultancy firm Joyce Advisory had been paid $1.1 million in public funds between 2019 and 2023.
"We understand the contractor's work is ongoing," he said.
Public organisations were typically required to invite multiple contractors into the procurement process to ensure that public funds were spent responsibly.
But Ryan said the University of Waikato did not engage in a competitive procurement process and had reached out to Joyce directly.
"Where there has been a direct procurement like this, and one that to date has cost well over $1 million of public money, we would expect to see a clear and documented reason for the services that were needed," he said.
"That explanation, and the assurance it would provide to the public that public money has been appropriately spent, is missing."
He said the matter was a "useful reminder" for public organisations to be transparent while hiring contractors.
The University of Waikato said it accepted the Auditor-General's comments.
"[We] will ensure any future variations to university policies will be reported to the University Council," a spokesperson said.
"The university accepts it is accountable for the expenditure of public money and for the outcomes resulting from that expenditure."
The spokesperson noted the process used to originally hire Joyce Advisory in 2019 was "permissable under the University's Procurement Policy and Independent Contractor Policy."
But it promised to "provide additional documentation when making future variations to contractor agreements, to ensure there is a robust reporting process".
RNZ
