The University of Canterbury dropped from 221 last year to 238 this year, and Victoria University of Wellington dropped from 237 to equal 265th this year.
Also making the list were Massey University, the University of Waikato, Auckland University of Technology and, for the first time, Lincoln University.
The University of Auckland also had the highest rankings for New Zealand universities by faculty.
It ranked 69 for Arts and Humanities, 78 for Life Sciences and Medicine, 89 for Engineering and Technology, 151 for Natural Sciences and 58 for Social Sciences and Management.
Ben Sowter, head of research at QS, said New Zealand's universities had collectively seen a drop in academic reputation, faculty student ratio and international students in this year's results.
The results revealed that average undergraduate tuition fees at the top 10 universities were up to a record high of around US$34,000 per year (NZD$42,395), nearly double the 2007 average of US$18,500 (NZD$23,070).
Mr Sowter said austerity measures in the wake of the recession had contributed to an "affordability crisis" for students at leading international institutions.
"With tuition fee hikes and student debt becoming a growing concern for both students and the New Zealand Government, the decline in affordable publicly funded education means many students risk being priced out of a world-class education."
Universities New Zealand chairman Professor Roy Crawford said New Zealand universities' slide was more the result of other tertiary institutions making big strides forward rather than our universities deteriorating.
"Although the New Zealand Universities are maintaining or in some cases increasing their scores ... they're slipping backwards because of the big moves forward by other universities in Asian countries and so on.''
However, he said it was concerning.
"It would be nice to say they (the rankings) are not important but they're very important.
"... But with Lincoln University on the list it means all eight of New Zealand's universities are now in the top 500 and I doubt if there are very many countries - if any - that could claim to have all their universities on that list.''
Tertiary Education Union vice president Sandra Grey said with the Government cutting hundreds of millions of dollars of tertiary education funding in the last five years, it was near impossible for New Zealand universities to maintain their places on the list.
"... Falling government funding means they face larger lectures and tutorials, more administrative workload that takes time away from research and teaching, and stagnant pay,'' she said.
A significant component of the criteria QS uses to rank universities is their staff/student ratio. Ms Grey said in New Zealand, staff/student ratios had risen from 17.5 students per academic in 2007 to 19 students per academic last year.
Tertiary Education Minister Steven Joyce said in a statement the results were "mixed news''.
"On the plus side it is the first time that all eight New Zealand universities are ranked in the top 500 in the world. On the other hand, some universities have had their scores improve but their rankings decline,'' he said.
"Overall the rankings reflect the increased competitiveness of the international university market.''
The Government had increased its investment in universities by 16.5 per cent over the last four years, despite tough financial times, he said.
Students had also increased their contribution through some increases in fees.
"Therefore as a country we are not likely to be able to afford big increases in resources, so the challenge for New Zealand universities from these figures is to respond more quickly and effectively to the competitive challenges they face. That includes growing international linkages and investing more in disciplines where they have a competitive advantage.''
The Government would address these matters further in the upcoming draft Tertiary Education Strategy.
The QS World University Rankings are made up of six indicators: academic reputation (40 per cent), employer reputation (10 per cent), faculty student ratio (20 per cent), citations per faculty (20 per cent), international students (5 per cent) and international faculty (5 per cent).
This year, 62,094 academic and 27,957 employer responses contributed towards the results.
1. Massachusetts Institute of Technology (MIT), United States
2. Harvard University, United States
3. University of Cambridge, United Kingdom
4. UCL (University College London), United Kingdom
5. Imperial College London, United Kingdom
6. University of Oxford, United Kingdom
7. Stanford University, United States
8. Yale University, United States
9. University of Chicago, United States
10= California Institute of Technology (Caltech), United States
10= Princeton University, United States
94. University of Auckland (down from 83 last year)
155. University of Otago (down from 133 last year)
238. University of Canterbury (down from 221 last year)
265= Victoria University of Wellington (down from 237 last year)
343= Massey University (down from 308 last year)
401 - 410. University of Waikato (down from 374 last year)
471 - 480. Auckland University of Technology (down from 451 - 500 last year)
481 - 490. Lincoln University
