The 44-year-old foe of Russian president Vladimir Putin felt unwell on a flight back to Moscow from Tomsk, a city in Siberia, Kira Yarmysh said on Twitter.
She said the plane made an emergency landing in Omsk, Siberia, and that Mr Navalny was suffering from “toxic poisoning”.
“He is in a coma in grave condition,” she said on Twitter.
She also told the Echo Moskvy radio station that Mr Navalny was sweating and asked her to talk to him so that he could “focus on a sound of a voice”. He then went to the bathroom and lost consciousness. He has been placed on a ventilator in an intensive care unit.
Ms Yarmysh said the politician must have consumed something from tea he drank earlier in the morning.
“Doctors are saying the toxin was absorbed quicker with hot liquid,” she tweeted, adding that Mr Navalny’s team called police to the hospital.
Anatoliy Kalinichenko, deputy chief doctor of the Omsk hospital where the politician is being treated, told reporters Mr Navalny is in grave, yet stable condition.
Dr Kalinichenko said doctors are considering several diagnoses, including poisoning, but refused to give details, citing a law preventing doctors from disclosing confidential patient information.
Last year, Mr Navalny was rushed to a hospital from prison where he was serving a sentence following an administrative arrest, with what his team said was suspected poisoning.
Doctors then said he had a severe allergic attack and discharged him back to prison the following day.
Mr Navalny’s Foundation for Fighting Corruption had been exposing government officials, including some at the highest level.
Last month, the politician had to close the foundation after a financially devastating lawsuit from Yevgeny Prigozhin, a businessman with ties to the Kremlin.
Last week, Belarus’ authoritarian president Alexander Lukashenko accused Mr Navalny of organising unprecedented mass protests against his re-election that have rocked Russia’s ex-Soviet neighbour since August 9.
Like many other opposition politicians in Russia, Mr Navalny has been frequently detained by law enforcement and harassed by pro-Kremlin groups.
In 2017, he was attacked by several men who threw antiseptic in his face, damaging one eye.
The most prominent member of Russia’s opposition, Mr Navalny campaigned to challenge Mr Putin in the 2018 presidential election, but was barred from running.
He set up a network of campaign offices across Russia and has since been putting forward opposition candidates in regional elections, challenging members of Russia’s ruling party, United Russia.
In the interview with Echo Moskvy, Ms Yarmysh said she believed the suspected poisoning was connected to this year’s regional election campaign.
Vyacheslav Gimadi, a lawyer with Mr Navalny’s foundation, said the team is requesting Russia’s Investigative Committee open a criminal probe.
“There is no doubt that Navalny was poisoned because of his political stance and activity,” the lawyer said in a tweet on Thursday.
Mr Navalny is not the first opposition figure to come down with a mysterious poisoning. In 2018, Pyotr Verzilov, a member of Russia’s protest group Pussy Riot, ended up in an intensive care unit after a suspected poisoning and had to be flown to Berlin for treatment.
Opposition activist Vladimir Kara-Murza was taken to hospital twice with poisoning symptoms, in 2015 and 2017. Both said they believed they were poisoned for their political activity.
