Several refugees have been evicted from their accommodation after the Afghan migrant allegedly violated the terrified teen.
The migrant, who is believed to be 16-years-old, is accused of grooming the child online from his room in Hollabrunn, Austria.
He remains in police custody in Korneuberg, according to the Salzburg Nachrichten newspaper.
A number of migrants had been offered accommodation in student halls at a technical college in the town following a deal with an Austrian refugee agency.
The furious Mayor of Hollabrunn has since cancelled the contract and kicked out the remaining migrants who had travelled from Afghanistan, Syria and Iraq.
Mayor Erwin Bernreiter said: "I have to take into account the worries of people and react in the interests of the majority of the population. In the building where the student accommodation is based there is also a kindergarten and a small child nursery."
He said it had been a tough decision to make, but he had acted in the interests of the parents of those who also shared the building.
He added: "I'm not prepared to wait until there was another incident before doing anything. I believe it is a risk with this group of asylum seekers."
Mr Bernreiter was backed up by local Freedom Party politician Christian Lausch, who said: "Right from the start we warned that something like this could happen."
Police in Lower Austria said the migrant first made contact with the child on social media in January this year.
He is accused of grooming her online and allegedly raped her in a wooded area before beginning a campaign of sexual abuse.
A police spokesman said: "The suspect did not use any violence, but he did threaten her and scared her into doing what he wanted."
"Over the course of three months the asylum seeker repeatedly sexually abused the schoolgirl." Her ordeal ended when, on the verge of a nervous breakdown over the situation, she had told her parents what was going on. They had immediately called the police, and the man was arrested. He is currently in investigative custody.”
According to German media the remaining 20 migrants from the shelter have been housed in accommodation across a number of districts in Lower Austria.
The decision to evict the migrants has divided the town.
Local Green Party politician Denis Thompson organised a demonstration in protest.
He said: "This whole thing reminds me of the Nazi policy of Sippenhaftung (where family members were made responsible for the crimes of their relatives).
"Until now there has been absolutely no problem with the other youngsters."
Fellow Green Party politician Peter Loy said that the decision to move the refugees meant that eight local helpers employed to care for the youngsters will also lose their jobs.
The alleged incident comes as tensions escalate in Germany over the migrant crisis.
Angela Merkel’s so-called ‘open door’ policy ha snickeringly come under fire in the wake of the Cologne sex attacks and there have been a number of reports of migrants carrying out sex attacks across the country, Express reported.
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