A Ministry for Foreign Affairs and Trade (MFAT) spokesman said it was understood the rule change would apply to all nationalities.
Last February, former Prime Minister John Key claimed a big diplomatic win when he signed a deal with his counterpart Turnbull to ease the path to citizenship for expats who arrived after immigration rules were tightened in 2001.
New Zealanders who had earned A$53,000 over five consecutive years would have been able to apply for permanent resident and a year later, for citizenship.
That new pathway will only become available in July and around 100,000 out of 305,000 New Zealand expats were said to be eligible for it.
The MFAT spokesman said New Zealand officials were "seeking clarity on how the proposed changes to citizenship rules will operate in conjunction with that pathway".
Victoria University researcher Paul Hamer, who has a special interest in New Zealanders in Australia, said the group of post-2001 arrivals appeared to be facing a new barrier to citizenship.
"They would have to show they had earned $53,000 for the past five years, then they would have to apply for the permanent visa which would take a lot of time and cost a lot of money.
"Now, they will have to sit on that visa for four more years before being able to apply for citizenship.
"So it becomes a 10-year process, whereas last year the announcement was that they would have to be on a permanent visa for one."
Hamer said the latest changes could be embarrassing for the Government, because Key came away from the talks last year "triumphant" about the gains he had made.
"And a year a bit later, here we are. I think it shows how powerless we are in the bilateral relationship.
"We get one step forward and then two steps back. We think we've got a gain, then a year or so later the rug gets pulled from under people's feet."
OzKiwi spokesman Timothy Gassin said the concessions secured by Key had been "gutted".
The latest immigration changes also affected another concession won by New Zealand in 2015 in relation to student loans for expats, he said.
"In effect any family that seeks to gain citizenship for their teenage children will find that these children become ineligible for student loans for a period of approximately five years between applying for the pathway and finally gaining citizenship," he said.
The announcement caught many Kiwis off guard because it came into effect immediately.
Kiwi rights advocate and lawyer David Faulkner said he was representing a Kiwi father of three who had lived in Australia permanently since 1999 and had a Resident Return Visa.
His client had planned to lodge an application for citizenship soon, but now would have to wait another three years before he could even apply.
"Understandably he's not happy. There's no rationale why somebody who's lived here for many years has to wait a further three years."
Faulkner said New Zealanders were worst-affected by the changes, despite the fact they were targeted at migrants from other countries.
"The vast bulk of migrants arrive here already holding permanent resident visas. So they're not touched at all. It's a handful of migrants.
"But virtually no New Zealanders migrate here on permanent visas. They only acquire them afterwards. So it's basically affecting every New Zealander applying for citizenship."
A spokesman for Australian Immigration Minister Peter Dutton did not specifically address questions about the impact on New Zealanders under the stricter citizenship rules.
But he said that Australian visa arrangements for New Zealanders were "more generous than those for any other country".
"The 1973 Trans-Tasman Travel Arrangement has allowed Australian and New Zealand citizens to enter each other's country to visit, live and work, without the need to apply for authority to enter the other country before travelling."
He added: "For the past five years New Zealand nationals have been in the top 10 nationalities of persons who have acquired Australian citizenship."
