Bastia – who sit 10th in the table after an impressive campaign – have risen to prominence in recent years under Hantz.
The 48-year-old helped the club from the third tier of French football to the top flight and after securing a 12th-placed finish in Ligue 1 last term, they look set to improve on that this term ahead of their final game at home to Nantes on Saturday.
Hantz said: "I couldn't get past that barrier. It was something very important to me.
"After that, being unable to resolve this issue, and after a lot of thought, I decided to call time.
"I believe that SC Bastia will continue to perform well, but knowing that they will do so without me there is an awful feeling.
"There are coaches who make their players grow, and then there are presidents who make their coaches grow as people.
"I spent a long time at Sporting (Bastia), and that's because I had a president who understood, helped and supported me."
"It has been an emotional week with Julien Sable and Mickael Landreau both hanging up the boots," he added.
"What's important for me is to prepare well for our final-day clash with Nantes. My professional connection with the club ends with the final whistle. After that, we'll see.
"I'm in the fortunate position of leaving the club on a positive note and I'm proud of the legacy that I'll leave behind me."
