Lanning returned to playing in January after taking an extended break from the game to manage her mental health and led Australia to the T20 World Cup title in South Africa during March before going on to feature in the inaugural WPL.
"It's an unfortunate setback for Meg and she's obviously disappointed to have been ruled out of the Ashes; it's a significant series for the team and she'll be missed, but she understands the need to put her health first," Shawn Flegler, CA's head of performance for women's cricket, said.
"Meg will remain at home where she will continue to work with medical staff with the aim to return to playing as soon as possible. We ask that Meg's privacy is respected at this time."
A CA statement added: "On the advice of CA medical staff, Lanning has been withdrawn from the squad due to a medical issue which requires management from home. A timeline for Lanning's return to play will become clearer in due course."
It will be the second Ashes series that Lanning has missed after she sat out the 2017-18 series in Australia due to a shoulder injury.
Lanning was part of the promotion of the fixture announcement for next summer little more than a fortnight ago.
Australia will not replace Lanning in the Ashes squad with Australia A touring concurrently for the first part of the trip meaning they can draft players in as required.