Flynn (75), an emeritus professor of political science and psychology at the University of Otago, ran the 3000m in 16min 6sec to take 54 seconds off the record in the masters men aged 75-79 grade.
"I'm very happy," Flynn said after the race.
"I thought I'd be doing well if I ran 16min 30sec. I didn't believe my time was possible."
Flynn came to New Zealand from the United States in 1963 and joined the Otago University staff four years later.
Though he first competed in athletics in the United States 64 years ago, the weekend's result was just the second record of Flynn's career.
He hopes to add the 1500m and 10,000m over the next few weeks.
Daniel Balchin (Caversham) sped round the final lap in 66sec to win the men's 3000m in 8min 46.83sec to beat Alex Gorrie (Hill City), who ran a personal-best time of 8min 48.74sec.
Anna-Lisa Uttley (Ariki) led from the start to win the women's 3000m in 10min 16.33sec from Sarah McLaren (Hill City), who improved by 13 seconds with her time of 10min 45.43sec.
Arthur Green (Taieri), a fourth-year physical education student, had a consistent series of throws, with four greater than 50m, when he won the men's javelin with 54.71m.
National junior champion Guy Archibald (Taieri), a student in sports performance at Otago Polytechnic, won the junior men's event with a throw of 53.14m.
Toby Flett (Hill City) won the men's sprint double with his 100m in 11.61sec and 200m in 23.12sec.
Lauren Wilson (Hill City) won the women's 100m in 12.79sec and the 200m 26.05sec.
Liz Wilson (Hill City), Lauren's mother, won the masters women's 100m 14.64sec and 200m in 29.21sec.
The Hill City 4x100m relay team of Zak Watt, Sam Watson, George Woodhouse and Chris McNoe broke the record for 13-year-old boys with a time of 51.76sec.
The team came together six years ago and they have broken the Otago children's records in their age group for each of the past five years.
This was their first open age-group record.
The third record of the day came in the pole vault, where Rosie Craven (Hill City) improved her own Otago girls aged-13 record by 5cm with a height of 2.05m.
The Paul Gibbons-coached athlete is a keen rock climber and has a head for heights, which enables her to be more aggressive when leaping upside down over the bar.
Callan Moody (Ariki) ran 56sec for the first lap but slowed to 60sec in the second lap when winning the men's 800m in 1min 56.05sec.
Hill City's Ben Jowsey (16) ran an encouraging 1min 59.39sec for second place.
