It followed a daylong standoff between his family and colleagues who had demanded he be evacuated while the doctors in the hospital in Omsk had refused to allow it, even after an air ambulance sent by Berlin-based nonprofit Cinema for Peace landed to pick him up. The Russian doctors had said his condition was not stable enough.
Navalny's colleagues, wife and personal doctor though had insisted he be allowed to leave and accused doctors of being pressured by the Kremlin to delay the flight in order to prevent the alleged poison used on him from being detected.
After almost 12 hours of arguing, the Russian doctors said they had acquiesced to the relatives' demands that Navalny be airlifted to Berlin's The Charité hospital.
"The patient is in stable condition, and having the request from relatives to allow him to be transported somewhere, we have at this point decided that we do not object to his transfer to another hospital, as will be indicated by his relatives," deputy hospital chief doctor Anatoly Kalinichenko told reporters, according to the Russian agency Interfax. He said the risk of allowing Navalny to fly was lowered now because his condition had "somewhat improved."
Navalny's spokeswoman, Kira Yarmysh, wrote, "It's a pity that to take this decision doctors needed so much time," saying the documents and plane had been waiting since morning.
Navalny's wife, Yulia, had earlier sent a letter formally appealing to president Vladimir Putin to give Navalny permission to be transported to Germany.
Navalny fell critically ill Thursday while flying from Siberia to Moscow, and was rushed to hospital after the plane had to make an emergency landing in Omsk. He has been in a coma in intensive care since then and attached to a ventilator. His colleagues allege his sudden illness is the result of poisoning, perhaps from a cup of tea he drank in the airport.
Doctors at the Omsk hospital though said they don't believe Navalny was poisoned, instead saying tests have shown no trace of toxins in his blood or urine.
"So at the present time, the diagnosis of poisoning, well, it probably remains in the back of our minds somewhere, but we don't believe that the patient suffered poisoning," deputy chief doctor Anatoly Kalanichenko told reporters earlier on Friday. Instead, doctors said that Navalny had suffered a "metabolic disorder," saying a sharp drop in blood sugar on the plane had caused Navalny to lose consciousness.
Navalny's colleagues and family have accused the doctors of concealing the real cause of Navalny's sudden illness under pressure from the Kremlin.
"The ban of transferring Navalny is an attempt on his life, which right now is being committed by the doctors and the lying government, which have sanctioned it," his spokeswoman Kyra Yarmysh tweeted early on Friday.
It is "needed only so as to drag out the time and wait so that it will no longer be possible to detect the poison that's in his system. Moreover, every hour of delay creates a critical threat to his life," she wrote.
Yarmysh posted photos of what she said were officers from Russia's FSB intelligence security service or Investigative Committee, the equivalent of the FBI, standing in the chief doctor's office. Navalny's wife earlier in the day said she was blocked from meeting with the German doctors by security agents in plain clothes who she said roughly removed her from the area near them.
The German medical team later said it had assessed Navalny and that they deemed him safe to transport. The chief Russian doctor, Murakhovsky, said the hospital didn't agree the flight was necessary, but accepted that it was possible now.
Earlier on Friday, the head of Navalny's group, the Anti-Corruption Fund, Ivan Zhdanov told reporters in Omsk on Friday morning that police had identified the substance used to poison Navalny but were refusing to tell his family its name. But Zhdanov said an officer had told them the substance was "very dangerous" not only to Navalny but also to those around him and that those near him were currently wearing protective suits.
Zhdanov said he and Yulia had been in the chief doctor's office when a police officer from a department sent to oversee his transfer to the German air ambulance entered.
"The representative of the transport police came in and showed the phone to the doctor saying that that substance was found," Zhdanov told reporters. "We asked the representative of the transport police who showed the phone to the doctor what was the substance found," he said, saying the police officer told them she could not tell them because it fell under secrecy rules of the investigation. But the officer said, according to Zhdanov, "It is dangerous not only for Alexey's life but for all people around him and all have to be in protective suits. She does not say more. We don't know what the substance is."
Later in the day, Omsk's regional police said traces of 2-ethylhexyl diphenyl phosphate, an industrial chemical, had been found on Navalny during tests on him. The chemical is used in food packaging and police said it was possible Navalny had been in picked up some of it from holding the plastic tea cup.
But doctors at the Omsk hospital later denied that the chemical had been found absorbed in Navalny's body, saying it was only on his hands and they had ruled it out as a cause of his poisoning.
Navalny, 44, is Russia's best-known anti-Kremlin opposition leader and is seen as perhaps Putin's most troublesome domestic critic. He has built a grassroots movement based around investigations, usually released as videos, that have exposed alleged corruption among top officials and some of Russia's most powerful business people, including members of Putin's inner circle.
A number of Kremlin opponents have fallen victim to poisoning in recent years, including the former Russian double agent, Sergey Skripal who was targeted with a nerve agent in the British town of Salisbury in 2018. Another prominent democracy activist, Vladimir Kara-Murza nearly died after being poisoned twice in 2015 and 2017. And two years ago, Petr Verzilov, a member of the protest group Pussy Riot, was evacuated to Germany to be treated for a near-fatal poisoning.
Navalny has been detained by Russian police many times as well as attacked by pro-Kremlin activists. Last year, he was hospitalized with what his colleagues said was poisoning after he suffered severe inflammation of his face while serving a short jail term for protesting.
A day earlier, the Kremlin's spokesman Dmitry Peskov had said it was ready to assist in Navalny being taken abroad if a request came. He said the Kremlin was aware of Navalny's condition had wished him a speedy recovering, saying if poisoning was confirmed, an investigation could be held.
Navalny's spokeswoman, Yarmysh, said they were now demanding the Kremlin fulfill that offer of help. She tweeted they would also appeal to the European Court of Human Rights to oblige Russia not to hinder Navalny's evacuation for treatment.
On Thursday, France and Germany's leaders, Emmanuel Macron and Angela Merkel, offered to have Navalny treated in their countries.
This report was featured in the Friday, Aug. 21, 2020, episode of “Start Here,” ABC News’ daily news podcast.
"Start Here" offers a straightforward look at the day's top stories in 20 minutes. Listen for free every weekday on Apple Podcasts, Google Podcasts, Spotify, the ABC News app or wherever you get your podcasts.