Most New Zealanders studying in Australia will pay about A$8000 ($8700) more from next year under a controversial shake up of the education sector, Foreign Affairs Minister Gerry Brownlee says.

But unlike international students, expatriate Kiwis will not face increases of up to 500 per cent, as initially thought.

Brownlee heads to Australia this afternoon for his first bilateral meeting with Australian Foreign Minister Julie Bishop tomorrow, and the latest changes to the education fees will be high on the agenda.

Many expats have been angered by the proposed changes, which are the latest in a series of measures affecting Kiwis and will require New Zealand citizens to pay full price for university.

Brownlee said the plight of New Zealanders had not registered in Australia because all students, including Australians, would be paying more from next year.

He gave further detail about the proposals, which had been described as a three-tiered system.

Australian citizens would pay a domestic fee rate, which would rise by between A$2000 and A$3600 a year for a four-year degree, beginning next year. About 2000 New Zealanders fall into this category.

Australian permanent residents from all countries and New Zealand citizens would 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 would be paying additional fees of A$33,000 a year, on average. This did not apply to New Zealanders.

The change was driven by a savings package in Australia's education sector worth around A$2.8 billion.

It was the third policy in two years affecting New Zealanders and introduced overnight with little or no notice to the New Zealand Government.

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.

Brownlee said the relationship had changed a lot since the days when New Zealand could cross the Tasman without a passport.

"For decades post World War 1, 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."