"There's been a long-standing assumption that all New Zealanders would own their own house but a lot of people now live in rental housing," she said.
"I wanted to provide evidence to support the premise that everyone should have the right to warm, dry, safe housing regardless of whether they own or rent."
The team has since worked around the country to address long-standing quality problems in housing, particularly as they affect vulnerable groups such as children, older people and those with chronic health conditions including asthma.
Through large scale community trials, involving around 10,000 New Zealanders, the team has demonstrated the effectiveness of initiatives such as retrofitting insulation to modern standards, installing effective and non-polluting heating and remediating injury hazards in homes.
The team evaluated the Warm-Up New Zealand programme, which itself was based on evidence from two of its earlier community studies.
The research showed that insulation or heating retrofits led to significant reductions in hospitalisations, the amount of medication required, energy consumption and premature deaths in people aged 65 and over.
A conservative estimate of the programme's net benefit has been shown to be around $950 million.
The work was also globally significant: in 2009, Professor Howden-Chapman was invited to chair the World Health Organisation's (WHO) Housing and Health Guidelines Development Group.
Dr Carlos Dora, co-ordinator of the WHO's Department of Public Health and Environment, described Professor Howden-Chapman and her team as "global leaders" in their area.
The International Energy Agency also considered the work "one of the most analytically robust and politically compelling" among the huge range of studies the organisation has reviewed.
"I feel very proud of what our team's been able to do," Professor Howden-Chapman said.
Prize winners
• Prime Minister's Science Prize, worth $500,000: Otago University Professor Philippa Howden-Chapman for her work to improve New Zealand housing conditions.
• MacDiarmid Emerging Scientist Prize, worth $200,000: Otago University researcher and lecturer Dr Karl Iremonger, who discovered a new brain cell structure and communication system, setting the stage for more targeted therapies for neurological diseases.
• The Science Teacher Prize, worth $150,000: Onslow College learning area leader for science Terry Burrell for an infectious love of learning which excites and stimulates both students and other teachers to perform at their best.
• The Future Scientist Prize, worth $50,000: Darfield High School student Tim Logan, 17, for his scientific investigations into the protection and survival of endangered indigenous plants.
• The Science Media Communication Prize, valued at $100,000: Auckland University biomedical and materials engineer "Nanogirl" Dr Michelle Dickinson, for her efforts to make the serious subject of science fun and accessible.