In that time the 36-year-old oversaw seven victories, one draw and four defeats, which resulted in a 22nd-place finish, two points above the drop.
The club have not confirmed the length of his contract, but they claim that he will "have the summer to build towards the 2017-18 season with the intention of putting this turbulent season behind us and looking to build on recent momentum and backing from the city".
Chairman of operations Gavin Foxall told the club's official website: "Michael has made the decision to appoint him on a permanent basis an easy one for the board of directors. From the outset as caretaker manager he has performed in an impressive manner in every area. His record and what he has achieved on the pitch in such a short period of time is phenomenal."
Flynn added: "I'm delighted to have been named manager of the club. Nothing makes me prouder than to take charge of my hometown club. I made no secret that I wanted this job. When I took over as caretaker manager in March, I said I felt ready for the challenge and that's still true now because I know this is a challenge.
"What we've achieved with this group of lads in the last few weeks has been unbelievable but I never want this club to be in that situation again. The challenge now is to get away, I'm ready to push on now and take this team forward with the help of Wayne Hatswell and Lennie Lawrence as well as the board."
Newport won just 12 of their 46 games in League Two.