Ranking editor Phil Baty said NZ universities rated well on research and publications, but fell behind in a global survey asking academics to rank the leading institutions in their fields.
"There is this really significant reputation lag. NZ universities are punching under their weight when it comes to their global reputation," he said.
"For some reason, the reputation of NZ universities is falling well below their research outputs."
He said the Asia-Pacific list was taken from data collected for last year's world rankings, in which Auckland University was ranked 165th-equal, up from 172nd in 2015.
However the weightings were adjusted slightly, with 5 percentage points less given to reputation and 5 points more given to income from industry - "recognising the younger profile of Asian institutions".
This made no difference to the rank order of NZ universities. Auckland ranked 24th, Otago 31st, Canterbury 54th, Victoria 58th, Lincoln 71st, Waikato 78th and Massey 85th.
Universities NZ director Chris Whelan said NZ research was widely cited in international journals, but academics did not think of New Zealand first when asked about institutional reputations.
"We do really well for citations in the international journals, but we are less top of mind to an academic in, say, Germany," he said.
He said Singapore topped the Asia-Pacific list, despite being a small country like New Zealand, because it had made universities a national investment priority.
"Singapore has been spending eyewatering amounts of money to go up the rankings. To them it's a national policy thing," he said.
"They have been spending millions of dollars on individual academics to attract the best.
"Can we do the same? My job is to say hell yes, wouldn't it be great to spend a lot more money on universities.
"But the reality is I'm a taxpayer too. We have a university system that is the most effective and efficient in the world. We are funded at 95 per cent of the OECD average, but we have every single university in the top 2.5 per cent of world universities."