The head doctor treating Mr Navalny said he was not well enough to be moved. But a spokeswoman called the decision "a direct threat to his life".
Activists in Germany have sent a plane to bring him to Berlin for treatment.
Mr Navalny is a prominent critic of Russian President Vladimir Putin.
He fell ill during a flight on Thursday. His team suspects something was put in his tea at an airport cafe.
The head doctor at the Siberian hospital, Alexander Murakhovsky, told reporters on Friday that Mr Navalny's condition had improved a little, but that he was still unstable. He said legal questions would need to be resolved before Mr Navalny could be moved.
But Mr Navalny's team said it was "deadly" for him to remain in the Siberian hospital.
"The ban on the transportation of Navalny is an attempt on his life, which is being made right now by doctors and the deceitful authorities who sanctioned it," Mr Navalny's spokeswoman Kira Yarmysh wrote on Twitter.
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WHAT KIND OF SPONSORED POSTS DO WE ACCEPT?
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Press release
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Video content
Article
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This kind of post is usually written to promote you or your business. However, we do prefer posts that naturally flow with the site’s general content. This means we can also promote artists, songs, cosmetic products and things that you love of all products or services.
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Every sponsored article will remain live on the site as long as this website exists. The duration is indefinite! Again, we will share your post on our social media channels and our email subscribers too will get to read your article. You’re exposing your article to our: Twitter followers, Facebook fans and other social networks.
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