It might involve offering input into programmes that were failing to be effective, or providing scientific information on ways to lift educational achievement.
"I'll be able to offer the Ministry independent advice and insights into what the scientific evidence might be suggesting."
While he admits the new role is one of his largest yet, Professor McNaughton is well qualified to tackle it.
As director of the University of Auckland's Woolf Fisher Research Centre, he has been developing education and schooling success for diverse communities, with research in New Zealand and in other countries.
In New Zealand, he has had a particular focus on boosting success in schools for children from Maori and Pasifika communities and children from low decile schools.
His most recent book, Designing Better Schools, identifies what was needed to be more effective in meeting the challenges faced by culturally and linguistically diverse students.
He supported concerns raised by Sir Peter Gluckman, the Prime Minister's Chief Science Adviser, around science literacy in schools.
"I really support the idea that we should be thinking about how to better teach science, and also how we can prepare children better about understanding and critically evaluating science in their everyday lives."
The three-year appointment comes as the Government is investing extra money to improve science in the classroom.
In November, it announced $3 million in additional funding to boost learning and teacher support across the science curriculum.
The National Monitoring Study of Student Achievement, released in the same week, found most Year 4 and Year 8 students' scientific knowledge was gained from listening to teachers rather than investigating their own questions or applying science to issues of concern to them.
Teachers working with Year 4 and Year 8 students reported they enjoyed teaching science, though some reported feeling less confident in their ability when it came to teaching science.
A month later, the OECD's Programme for International Study Assessment (Pisa) report revealed New Zealand had fallen from 7th to 18th in international rankings for science.
"The Pisa data told us that other countries were gaining in maths and science, but also, as with others, we are slipping in our achievements," Professor McNaughton said.
On the positive side, he added, our education system had many strengths to play to.
"We don't know all of these bits that make a difference, but many of them, and it will be a matter of putting them together in a way that will have an impact nationally," he said.
"Ultimately, I'll feel that I will have contributed if the role has helped to make a difference to those challenges with achievement, and that there are good discussions and use of scientific evidence to make policy."
Secretary for Education Peter Hughes said the appointment marked "a major development in education".
"I'm looking forward to seeing how he can push boundaries, ask the tough questions, and dig deep to get important answers."
Prime Minister John Key described Professor McNaughton as a "very talented and capable individual".
"We think it's a great idea to be focussing on science for our youngsters," he said.
"I think we can always do better, the main thing is to encourage more youngsters to be actively interested in science - it's very important for our economy, and it's very important for how we can perform as a country."
