The former Highlanders coach and All Black and Otago fullback was contracted until June 2019, but has left the Paris based club by mutual agreement to return home to his family.
Cooper will return home after Stade Francais' match against Pau on January 27.
Cooper's youngest daughter fell ill late last year and will have an operation in a few weeks.
Cooper told the French website, Rugbyrama, that he'd found it too difficult to be away from his family and wanted to be by his daughter's bedside.
"My daughter's health is not good," he told Rugbyrama.
"She was hospitalised for a few weeks in New Zealand and I can't handle this situation 20,000km away.
"I didn't want these personal concerns to interfere with my job as a coach.
"After the match against Pau I will go back to New Zealand to take care of my child."
Cooper's wife had been travelling back and forth between Paris and New Zealand but has remained in Dunedin since October.
Cooper has worked as a coach in France since July 2016, but said it was time to return home after the situation became difficult.
"The health of my little girl is precarious for a long time," he said.
"She was not good when I was training in Japan. But there, the season was not so long, the jet lag less important."
"I could talk with my daughter almost continuously, and when she really needed to see me, I jumped on a plane."
"All of this is more difficult from Europe."
The 52-year-old said his focus will now be on the health of his daughter, but would like to return to coaching in the future.
Cooper previously coached the Highlanders and was the assistant coach for the Blues.
