"He has spent the past 17 years studying biodiversity across terrestrial and marine environments," EPA chief executive Dr Allan Freeth said.
"A recognised expert in genetics, he has maintained a strong connection to New Zealand through co-operative work with colleagues in academic and government agencies."
Bunce said he was honoured to join the authority.
"This opportunity will enable me to translate some of my research in environmental and biodiversity monitoring into the scientific decision-making of New Zealand's environmental authority."
His appointment follows the controversial 15-month tenure of former EPA chief scientist Dr Jaqueline Rowarth.
She left the authority in February last year after concerns from the Prime Minister's chief science adviser and Environment Ministry that her public statements were undermining the authority's credibility.
Her outspoken comments included criticism of a freshwater scientist, dismissal of scientific concerns about a prominent weed-killer, and describing irrigation as a "great boon" to the environment - which outraged environmentalists.