University of Auckland professor of physics Shaun Hendy said this country's position in the latest index was a "fair indication" of its place in the world, but the decline from its 2012 ranking was disappointing.
A lower score in the human capital category was one driver of the drop, Hendy said.
The latest report said this country had 6339 researchers per one million of population, down from 7017 in the 2012 index. New Zealand was ranked 11th in the world for researcher headcount this year, compared with 7th last year.
"There's still a brain drain," Hendy said. "We're still losing researchers overseas."
In the overall human capital and research category, New Zealand was given 54.9 out of 100, down from 57.6 last year. This country was also given lower scores in the technology output and business sophistication catagories compared with 2012.
The report said Iceland was the top-ranked country in terms of researcher headcount, with a result of 13,101 researchers on a per million of population basis.
The lowest-ranked nation was Niger, in West Africa, with 10 researchers per million.
The index uses 84 indicators, including quality of universities, venture capital deals, microfinance and researcher headcount to rank the 142 countries.
New Zealand was one place ahead of South Korea, the home of Samsung, in the overall rankings this year.
Hendy said South Korea was very innovative in certain fields, but still had a "way to go" in terms of having a "broadly effective science and technology system".
New Zealand achieved higher scores than South Korea in a number of categories, including creative output, market sophistication (such as ease of starting a business) and institutions.
However, the Asian country scored higher than New Zealand in other areas like technology output and human capital.
Technology commentator Peter Griffin said it was a good sign that New Zealand had made it into the "leader's category" of the latest innovation index.
"But we're an inefficient leader as well," Griffin added. "For the amount of effort we're putting in we're not getting the expected returns."
New Zealand's efficiency ratio - calculated as the ratio of the output sub-indexes over the input sub-indexes - was just below the median level.
"We're putting increasing amounts of funding into science and basic research as well as applied science, but we're not getting the outcomes you might expect," Griffin said. "That has something to do with our poor track record on productivity ... I think that drags us down in a lot of these global rankings."
He said the science sector in New Zealand was becoming more "integrated", which was a positive development.
"We've got a lot more collaboration and clustering going on with researchers clustering around big companies like Fonterra," Griffin said.
Hendy wasn't surprised that the United States only achieved 5th place in 2013 index.
"This is a national measure and of course there's lots of different parts of the US that go in," he said. "If you looked at California [where the Silicon Valley is located] no doubt it would rank highly."
New Zealand was ranked 28th in an index of the world's 50 most innovative countries compiled by the Bloomberg news agency earlier this year. The US topped that list.
