The Putin critic is serving a 30-day jail sentence for calling a mass protest after authorities blocked prominent opposition candidates from taking part in Moscow city elections.
His spokeswoman Kira Yarmysh on Sunday said he was receiving treatment for a "severe allergic reaction".
His personal physician Anastassia Vassilieva later said on Facebook after visiting Navalny in hospital that he was suffering with swollen eyelids and multiple abscesses on his neck, back, torso and elbows.
"We can't rule out that his skin has been exposed to a toxin and been damaged by an unknown chemical substance from a third person," she said, adding that Navalny has never had any allergies.
Ealier in the day Yarmysh said the source of the allergic reaction had not been determined.
"He is currently in the ward under the supervision of police officers. He is being provided with the necessary medical assistance," she added.
Navalny hoped to stand against President Vladimir Putin in an election last year but was barred because of a fraud conviction he and supporters say was politically motivated.
The 43-year-old has served several short jail sentences over his protest activity.
Two years ago, Navalny had to travel to Spain for surgery after a street attack left him nearly blind in one eye.
Sunday's hospitalisation came a day after almost 1,400 people were arrested at the demonstration the opposition leader had called.
Leonid Volkov, Navalny's former campaign manager, said he had a similar reaction after he served a sentence in the same cell last month for violating protest laws.
He rejected talk of a "conspiracy", calling instead for a "serious inspection" of hygiene standards at the jail, in a tweet posted Sunday.
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