The Toulouse player picked up the injury to his right ankle during his side's 64-22 victory over Narbonne in the Top 14 last weekend.
"Medical examinations have revealed the player has fluid on part of his ankle, which is the result of previous injuries," said Stade Toulousain doctor Albert Sadacca.
"This is not a major injury but he needs time to rest and recover."
Michalak is not expected to be back in action before the end of October.
National team coach Bernard Laporte is expected to announce his squad on October 25 ahead of the four November Test matches against Australia, Canada, Tonga and South Africa.
France's talented 22-year-old centre Benoit Baby also sprained his left knee in the same match, and will be out of action for up to eight months.
"My thoughts go to Benoit who been plagued by serious injuries," said Laporte in L'Equipe.
"Considering his young age I feel very sorry and sad for him."
Laporte, though, admits he has doubts about selecting Michalak for the Autumn tour.
"Eight weeks will have passed between the day he injured himself and our first Test match against Australia on November 5," said Laporte.
"I must find out about the exact gravity of the injury as well as about his recovery programme.
"I don't know if he will have trained enough before resuming competition with his club.
"In fact, if Fred plays with his side in the European Cup against Wasps on October 29, then his name should be on the list."
Fellow fly-half Yann Delaigue is also a doubt as he has not played in five months because of a shoulder injury.
"For Yann, I don't know," added Laporte.
"He has not played since mid-May, that's a long time without any competition."
Julien Peyrelongue, David Skrela, Benjamin Boyet and even Saracens' Thomas Castaignede are possible candidates to replace Michalak in November.