His third placing from grid 16 in his second heat was crucial in his quest for a podium finish. Flynn finished fifth from grid seven in his third and final heat on Friday night.
Wet weather on Saturday night forced the second half of the championship to be postponed until Sunday night.
"The track was quite rough on Sunday night and it chopped up a bit because of the rain," Flynn recalled.
However this didn't stop Flynn from driving his 422 Chev-powered Hypermac to second place from grid eight in his fourth heat and fourth place from grid eight in his fifth. This qualified him second on points before the final for the top 20 qualifiers.
Top qualifier and eventual title winner, Mt Maunganui's Sam Waddell, opted to start from grid two in the final, which gave Flynn pole.
"Sam and I cleared out early but the first yellow closed the field up again. From then on it was a case of trying to be patient and we had to be cautious when we got caught up in lap traffic," Flynn explained.
At one stage in the final Flynn's brother, two-time national champion Steve Flynn, got to eighth place from grid 17. He finished 19th after being one of three drivers who didn't finish the final as he ended up in the wall. Waddell, a son of two-time national champion Dean Waddell, won the Meeanee-hosted round of the Burger King-Pro Dirt Series in December. He was one of two Mt Maunganui drivers to make the podium at the weekend as defending champion Steve Cowling finished third.
Flynn came fourth in the series, which finished in Palmerston North this month and was won by Cowling's brother Chris. Steve Cowling was second and Waddell third.
Flynn will race in the Taranaki championship at Stratford on March 21 as well as in the remaining Meeanee meetings this season. With his second placing at the weekend it means the Flynn brothers have made the podium in the national championship five times. Steve won the championship in Nelson during the 2011-12 season and in Wellington during the 2014-15 season. He also finished third in Auckland during the 2013-14 season.
Meanwhile Hawke's Bay's four-time national solobike champion Bradley Wilson-Dean will be out of action for the next six months after surgery on an injured shoulder.
"I've been instructed by the surgeon and bone specialist that if I want to heal properly then I can't be racing any kind of bikes for at least the next six months," Wilson-Dean said from his United Kingdom base at the weekend.
"It's been really tough on me not just physically but mentally as well and the decision to sit out wasn't one I made lightly So I must say thank you to all of my supporters and to my clubs Peterborough & Somerset for being so understanding, supportive and for caring about my wellbeing over all other things," Wilson-Dean added.