Northern eventually declared their innings closed at 533-6 when Flynn was dismissed for 182 after blasting 17 fours and half a dozen sixes.
Flynn's century - his 11th for Northern Districts and 12th in first-class cricket - saw him take sole ownership of the most centuries for the domestic side as he moved past Graeme Hick who registered 10.
Flynn will shortly join the Black Caps for their two-test series against Sri Lanka in the sub-continent and yesterday's knock confirmed the 27-year-old will head overseas in good form.
Northern's mammoth second innings meant that despite recording a first-innings deficit of 94, they set Otago 440 to win.
Otago found the going tough late in the day's play as they were put in to bat with 10 overs left in the evening.
They lost openers Aaron Redmond and Hamish Rutherford who both fell to the bowling of James Baker.
At the close of play Otago were 12-2 with Michael Bracewell unbeaten on four and night watchman Neil Wagner also at the crease on five, while Baker finished with 2-7 from five overs.
In Napier, Central Districts are in control of their match against Auckland at Nelson Park. After Auckland began the day at 80-4 in their first innings they were bowled out for 210. Central Districts captain Kieran Noema-Barnett enforced the follow on and Auckland finished the day on 210-7, still 10 runs behind.