But the day belonged to Flynn, putting his side in charge with his 15th first-class ton and preventing Kyle Mills (0-57) from enjoying any success in preparation for the five-match ODI series against the West Indies.
Elsewhere, bat also trumped ball in the top-of-the-table clash at Karori Park in Wellington, although a couple of late wickets saw the hosts claw their way back against Canterbury.
Tom Latham enjoyed a day almost equal to Flynn's, seizing the initiative after being sent in and scoring 137 to see his side through to 292-5 at stumps.
Latham was overlooked for the Black Caps' one-day squad announ-ced earlier this week and he batted like he had a point to prove, sharing significant stands with Henry Nicholls (70) and Shanan Stewart (60).
Before the dismissal of Stewart, Canterbury progressed to 290-3 and looked in control, but two wickets from Andy McKay in the day's penultimate over gave the home side some hope heading into day two.
But Canterbury will still be confident of amassing an opposing first innings total and adding to their lead atop the Plunket Shield standings, with Latham set to resume eight runs shy of his career-best score.
The day's trend was bucked in Dunedin, where Jesse Ryder helped Otago's bowlers run through Central Districts for 255 to snatch control at University Oval.
Ryder, set to open the batting for New Zealand on Boxing Day, showed his all-round abilities when his two early wickets reduced CD to 67-3. Things soon got worse for the Stags as they saw three batsmen depart with the score locked on 76, eventually managing a respectable total courtesy of Kruger van Wyk's 91.
In reply, Otago couldn't survive a tricky nine overs before stumps, losing Aaron Redmond (5) and Michael Bracewell (4) to close on 30-2.