But Brownlee said New Zealand protests had not registered in Australia because the changes affected local students as well, although not to the same degree.
"The reason this hasn't registered as an issue in Australia is because every Australian student in a tertiary institution will be paying more."
With the higher fees all but set in stone, the bilateral talks are likely to focus on whether there are more changes in the pipeline which could penalise New Zealand expats, and the need for Australia to "communicate sooner" about policy changes which affected Kiwis.
It was the third policy in two years which penalised New Zealanders, all of which had caught the Government off guard, Brownlee said.
In November 2015, Australia revoked the visas of some ex-criminals no matter how long they had lived in Australia.
It forced New Zealand to quickly change the law to allow the flood of deportees to be monitored when they returned.
Two weeks ago, Australia announced stricter citizenship rules, lifting applicants' wait-times from a year to four years, again without notifying New Zealand.
And on Monday, Australia released its proposals to raise fees in universities. It was another surprise for Prime Minister Bill English, who had not been told of the change despite speaking to his opposite Malcolm Turnbull on Friday.
English said on Tuesday he has since exchanged text messages with Turnbull about the education cuts.
Australians pay the same for university study in New Zealand as Kiwis. They can get access to student loans after living here for either two or three years.
Brownlee said the latest changes were "not a basis for a collapse in the relationship". But he said the traditional alliance had changed significantly since the days when New Zealanders could cross the Tasman without a passport.
"For decades post-World War I, the two countries treated each other's citizens the same as if they were at home, very little difference.
"It's sort of been a slow progression to the separate, sovereign state sort of stuff."
New Zealand First leader Winston Peters, however, said New Zealand should be apologising to Australia.
He said New Zealand had become a "bolthole" for people wanting to get into Australia through the back-door, and this had influenced the ongoing crackdown on Kiwis.
Aussie changes: Who pays what?
• Beginning next year, Australian citizens will pay a domestic fee rate, which will rise by between A$2000 ($2165) and A$3600 a year for a four-year degree. About 2000 New Zealanders fall into this category.
• Australian permanent residents from all countries and NZ citizens will pay full fees; an average increase of A$8000 to A$9000 a year. About 6000 New Zealanders are in this category.
• There is also a rate for international students, who will be paying additional fees of A$33,000 a year, on average. This does not apply to New Zealanders.
