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He ran 7min 59.34sec at the Potts Classic in Hastings, a race which doubled as the national championships.
It left him 0.06sec ahead of the record former Olympian Dick Tayler set 50 years ago.
Chignell finished sixth in what was a fast-paced race.
Tauranga’s Sam Tannerwon in 7min 54.16sec, edging Napier’s Eric Speakman by half a second.
Chignell was part of a group of seven who separated themselves from the field early.
They remained close before Tanner kicked in the final lap, forcing the pace and proving too much to keep up with.
The record goes with the new 5000m mark Chignell broke before Christmas.
Meanwhile, Rebekah Greene, also of Hill City-University, ran her fastest 800m since 2014 in an impressive display. Her time of 2min 07.73sec took her to victory in a strong field.
She led at the halfway mark, before accelerating away down the back straight.
No1 ranked New Zealander in the event, Katherine Camp, attempted to close the gap over the last 200m, but Greene showed great strength to hold off the Canterbury runner.
At the Caledonian Ground on Saturday, at an Athletics Otago meeting, Christchurch Old Boys’ Dylan Forde ran 4min 01.12sec to edge HCU’s Jared Monk by just over a second in the 1500m.
HCU’s Cameron Moffitt delivered a strong 400m time of 51.63sec, while Nathan MacDonnell and Tamsin Harvey ran 11.15sec and 12.58sec in the men’s and women’s 100m respectively.
Taieri’s Cole Gibbons won the open men’s pole vault with a height of 3.6m.