The Ireland hooker, who missed out on the 2009 Lions tour due to another injury, has been sidelined for the vast majority of this season and has racked up just 53 minutes of rugby.
Flannery underwent calf surgery in March and is set to return to action in time for the showpiece tournament but he will be desperately short of match fitness.
It has already been reported that fellow Ireland international Rob Kearny may look to the Southern Hemisphere for game time and McGahan has admitted he would approve to a similar move for Flannery.
"Jerry is a contracted Irish Rugby Union player, this is our last game of the season and Jerry obviously has no chance of playing," said McGahan.
"Whatever is the best opportunity for Jerry to get fit for the World Cup we would endorse it."