The country's universities say securing more government funding is key to avoiding cuts that will harm education and research.
A briefing from the Tertiary Education Commission to incoming minister, Penny Simmonds, warned higher education and research were at risk from university cuts.
Universities have been looking at job and in some cases course cuts to save money.
The briefing, released publicly on Thursday, said the situation was unprecedented.
It said universities were financially stressed from the loss of foreign enrolments during the past four years, falling domestic enrolments, and government funding that has not kept pace with inflation.
Universities New Zealand chief executive Chris Whelan told Morning Report government funding was a big issue.
"Effectively over just the last three years, inflation has gone up by about 17.1 percent, but Crown funding has only gone up by 5.5 percent.
"Long run, the Government has tended to keep funding for universities broadly in line with inflation, this is the first time in 20-something years that we've fallen dramatically behind."
Whelan said 80 percent of universities' funding came from the government.
He said they'd had a brief meeting with the new minister late last year but were looking forward to another meeting soon.
"There's an awful lot on the desk of the new minister and it's going to take a little bit of time for us to be able to work this through."
The briefing also raised the need to tackle disparities for Māori, Pacific and disabled students across all levels of education.
Whelan said universities took also took disparities very seriously, but he said tough financial settings could make it hard to get the correct support in place.