Flynn brought up his century yesterday with a pull shot over midwicket and worked the ball around the ground in a chanceless knock.
It put Northern Districts in a strong position on day three of the rain-affected match as they look to maintain their position at the head of the Plunket Shield table.
They declared their first innings closed on 351 for eight, with Flynn moving through from 68 not out, and Auckland were 39 for one in reply.
The second day on Monday was washed out and play began yesterday at 2pm, leaving Auckland a massive task to try to overhaul Northern on the points table and win the Plunket Shield.
Both sides picked up three points from Northern's innings, meaning the Knights maintained their 15-point gap on Auckland, and the Aces will need to produce something special to overhaul the margin.
Auckland play Canterbury in the final round of the competition starting on Monday, with Northern Districts playing Central Districts.
Flynn and Northern Districts teammate Trent Boult were due to meet up with the rest of the New Zealand squad last night.
Tim Southee, playing in his first domestic match since being axed for the second test, picked up the early wicket of Brad Cachopa, with opener Jeet Raval on 10 and Neal Parlane six at stumps.
Otago fell two runs short of Canterbury's first-innings total when they were dismissed for 197 at the University Oval in Dunedin.
They looked on course for a first-innings lead when they were 178 for six and with Sam Wells (52) and Derek de Boorder (32) at the crease, but lost their last four wickets for 19 runs.
Willie Lonsdale picked up three wickets (3-58) and Ed Nuttal two (2-42), but leg spinner Todd Astle picked up the valuable wickets of Wells and Neil Wagner (10) to give Canterbury a slim advantage.
Canterbury were 119 for three in their second innings, a lead of 121 runs heading into the final day. Tom Latham is unbeaten on 38.
No play was possible in Wellington's match against Central Districts in the capital, with Central one without loss in reply to the hosts' 501 for six declared.