They blame the country's image as a "scientific backwater" and the demands the NCEA places on science students compared with those studying other subjects.
Science teachers nationally have noticed the decline and Otago Boys High School head of science Allan Garbutt said evidence suggested it was a trend also affecting the western world and Asian countries.
At Otago Boys High School, there were six physics classes 20 years ago.
Now, there were two or three, he said.
Chemistry numbers had also declined, but not to the same degree, and biology remained steady because it was an important prerequisite for medical school and other health sciences.
Mr Garbutt believed the decline of between 30%-50% of pupils taking NCEA level 1-3 sciences was because of changing attitudes towards science as a career.
"When I was growing up in the 1960s and '70s, science was big. The Cold War was big, space exploration, the Vietnam War and general technological advancements were all in the public eye.
It was a time of huge curiosity. Science was a prestigious career."
Today, science careers and their salaries were not like they used to be, he said.
Part of the issue was that New Zealand was "a scientific back-water", he said.
"There's nothing here. Scientists have to spend more time looking for funding rather than doing their research. It's not encouraging young people to become scientists."
NCEA may also be contributing to the problem, he said.
Biology, chemistry and physics subjects were demanding at NCEA levels 1-3.
They required much work and discipline from pupils and many avoided the subjects.
"The kids aren't stupid. They've worked out the easiest way to get their NCEA qualification.
"They take the easy options."
Logan Park High School head of science Murray Thompson said he too had noticed a decline of about 30% in the number of senior pupils studying sciences in the past 20 years, and worried about the implications for New Zealand society.
"The vast majority of people don't understand the science they are totally dependent on.
"People say chemistry is bad. When was the last time you took medication - that's chemistry.
"Science doesn't create pollution - it cleans it up. If we don't continue science, we're going to have huge problems."
Otago Girls High School acting head of science Ian Phillips agreed.
A poor level of scientific understanding "hinders our ability to make educated decisions about our future, in particular with regard to climate change, the environment, medical advancements and technological advancements".
"All the solutions to the world's problems are all to do with science."
Science was compulsory in all schools up to year 10 and Dr Phillips believed a solution to the problem may be to make it compulsory up to year 11 (NCEA level 1).
General science was compulsory for year 11 pupils at Otago Girls High School.
The girls were actively encouraged to continue science and he believed the practice had contributed to the stable number of pupils continuing science subjects into year 12 and 13 at the school.
