Vodianova, who has been the face of Calvin Klein campaigns and modelled for Givenchy and Stella McCartney, grew up in poverty in the industrial city of Nizhny Novgorod, where her sister and mother still live.
She wrote an indignant Facebook post after her 27-year-old sister Oksana, who has autism and cerebral palsy, was ordered to leave a cafe with her carer on Tuesday, with the owner allegedly claiming they were frightening other customers.
Hours after Vodianova's post, Russia's Investigative Committee opened a criminal case into violation of human dignity with the threat of violence, which carries a maximum jail term of five years.
The case has garnered extensive media coverage in a country where the rights of people with disabilities to equal treatment and access are still far from fully recognised.
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Vodianova wrote on her Facebook page yesterday: "The owner of the cafe suddenly came up to them and said, 'Get out of here, you are scaring all our customers. Go get treated and treat your child, then you can go out in the public.'"
When the women refused to leave, a security guard threatened to commit them to a psychiatric institution, she said.
The cafe owner's son told Russian state television that Oksana was frightening customers by "banging her head against the wall."
Vodianova is a long-time advocate for the rights of disabled people and launched the Naked Heart Foundation in 2004 to support special needs and underprivileged children in Russia.
The 33-year-old model also served as an ambassador for last year's winter Paralympic Games in the Russian Black Sea resort of Sochi.
"What happened to my sister Oksana... Is not an isolated case. This is unfortunately the reality all families raising children with special needs experience," Vodianova wrote.
Russia has made attempts to improve the treatment of people with disabilities, especially ahead of the 2014 Olympics and Paralympics in Sochi.