His comments come as statistics released by the Government over the past few months show the proportion of men in tertiary education continues to drop, with men making up 42.6% of domestic students at polytechnics, universities and other providers in 2011, compared with 44% the year before.
The figures showed the number of New Zealand men enrolled in tertiary education in 2011 stood at 163,366, down 19.65% from a peak of 203,326 in 2006. In comparison, there were 220,103 women in tertiary education, down 13.07% from the record 253,202 in 2005.
The gap was also present at Dunedin institutions, with women making up 61.52% of students at Otago Polytechnic and 56.53% at Otago University.
Prof Flynn, who has researched IQ differences between men and women, said the gap showed ''something is going wrong'' in secondary education, with boys faring significantly worse at high school than girls.
''That's why you find there are more women at university. A guy with an IQ of 100 is likely to Bs and Cs, a girl with an IQ of 100 is likely to get As and Bs and think of herself as university material,'' he said.
As a consequence, New Zealand was ''wasting a lot of male talent'' and something should be done about it, he said.
''I think any Government should be alarmed at the tremendous gap in performance according to gender at secondary schools,'' he said.
Prof Flynn said New Zealand was not alone when it came to boys underperforming at secondary schools. The problem was prevalent throughout the world.
However, he was sceptical about solutions proposed by some, which included having more same-sex schools for boys and having a less structured education system.
The Ministry of Education did not reply to questions on what it was doing to address the performance of boys at secondary school, instead pointing towards a 2008 Education Review Office report on the issue.
In the report's introduction, the author states that: ''Educational research on boys has not provided definitive advice to schools about how they can improve their teaching practice to further support the achievement of boys''.
A spokesman for the ministry also pointed out statistics which showed that in New Zealand in 2011 only 38.5% of male secondary school pupils left with university entrance standard, compared with 52.6% of females.
The difference was even greater in the Otago region, with 42.3% of males leaving school with university entrance, compared with 62.7% of females.
Prof Flynn said women particularly outperformed men when it came to reading and writing.
This meant women were beginning to outnumber men in professions where literacy was important, such as journalism, law, psychology and lower level management.
''Even medical school now has a female majority, I am told,'' he said.
When it came to why there were not more women chief executives, Prof Flynn said: ''Well there, of course, other things come in.''
''That is, many men are driven and they will work a 72-hour week and ignore their family and friends to get to the top.
''Thanks to being a bit more sane and also the presumption that they will be more involved with children, women, of course, hit to some degree a glass ceiling,'' he said.
Dan Reddiex, the rector at King's High School, which last year had the highest NCEA pass rates for state boys' schools in the country, said there were a few key ways of getting boys to perform.
They included creating ''a competitive environment that encourages success'', setting high expectations to avoid the ''minimalist mentality that NCEA has the potential to breed'' and catering specifically for the preferred learning styles and needs of boys.
When asked if the gap was considered a problem, Tertiary Education Minister Steven Joyce replied by email, saying: ''The increasing number of female students in tertiary education is part of a continuing trend internationally.''
''I would encourage any student, male or female, to make the most of their opportunities for tertiary education.
''The career market worldwide is becoming more competitive and those students with higher levels of skills and talents are increasingly in demand,'' Mr Joyce said.