The Tertiary Education Commission (TEC) is investigating Lincoln University and the West Coast's Tai Poutini Polytechnic.
The reviews are the latest in a series of investigations that have recovered millions of dollars from institutions that breached their funding conditions, but are the first to involve a university.
The commission said the Lincoln review involved the university's Telford division, which was formerly a polytechnic.
It said it had concerns about whether the division stuck to its funding conditions when delivering some of its courses.
The commission said the investigation at Tai Poutini was because of discrepancies found by a regular audit in 2015.
TEC chief executive Tim Fowler said Deloitte had been selected to run the inquiries.
"In both these cases we upgraded to an investigation after earlier monitoring indicated we needed to take a more thorough look," he said.
"There is a message here for all tertiary education organisations. We have a sophisticated and effective monitoring framework. If you are not meeting your obligations, we will find out."
A Lincoln University spokesperson confirmed the investigation into a sample of Lincoln's programmes.
"We understand that the investigation is as a result of TEC's monitoring processes to ensure that delivery matches the funding universities receive from TEC," the spokesperson said.
The chairperson of Tai Poutini's council, Graeme McNally, said the institution had itself spotted possible problems and alerted the commission last year.
"In 2014 TPP had commenced its own internal review of TEC/NZQA requirements and had "self-declared" to the Tertiary Education Commission in 2015 some potential non-compliance. It subsequently adjusted the funding it claimed for a small number of programmes."
The commission has previously warned institutions that they must stick to the rules for their government funding following a series of breaches.
In October 2015, the commission ordered Agribusiness Training to repay $6.24 million after an investigation found it was teaching fewer hours than it was being paid for.
In September that year, it ordered another private agriculture training business, Taratahi, to repay $7.5m for delivering less education than it had been paid to provide.
In 2014, a polytechnic, the Western Institute of Technology at Taranaki had to repay $3.7m and Te Whare Wananga o Awanuiarangi was told to give back $5.9m.