The Berlin-based Cinema for Peace Foundation had sent a plane with a team of medical professionals to Omsk in an effort to move Navalny to the Charite Hospital. The jet had been waiting on the tarmac. The critical care transport left the hospital with Navalny at about 5:15 a.m. local time (23:15 GMT) on Friday.
A Sputnik correspondent later reported that the medical jet with Navalny on board had taken off from the Omsk Airport.
On Friday, Omsk doctors gave the greenlight to allow Navalny to be transported to Germany for treatment after he fell gravely ill and went into a coma during a domestic Russian flight on Thursday.
Navalny's supporters suspect he was poisoned, while the head doctor of the Omsk hospital put his condition down to a metabolic disorder.