May Cavanagh gained the top mark in media studies, Ambryme Guergoua was top in the French examination and Sylvia Otley was top in sculpture.
The trio will receive Top Subject Scholar awards at a ceremony at Parliament later this year.
They all said the awards were a surprise because it had been a very busy and distracting year, following the Covid-19 lockdown.
May said the Covid interruption had forced them to focus on their NCEA qualifications first and foremost.
Going into the scholarship exams, there was a feeling of "if I get one, it will be a bonus", she said.
Sylvia said when results were released, she was preparing herself for the situation where she did not receive a scholarship.
"To find that we got the top marks in our exams was a bonus on top of a bonus."
Kavanagh College pupil Tobias Devereux and King’s High School pupils Samuel Blackwood and Aaron Hewson received Outstanding Scholar Awards for being among the top 40-60 candidates who achieved some of the highest marks in three or more scholarships.
They were among more than 10,400 pupils across the country who sat the examinations last year, and among 2148 who were awarded one or more scholarships across the 36 subjects.
NZQA assessment deputy chief executive Kristine Kilkelly said New Zealand Scholarship exams assessed pupils on their ability to demonstrate high-level critical thinking, abstraction and generalisation.
"New Zealand Scholarship is regarded as the most prestigious secondary school award in the country," Ms Kilkelly said.
"It is designed to challenge the very best students and offers financial rewards for those going on to full-time tertiary study in New Zealand."
