"Three persons have been arrested in this connection so far," Inspector General of Police (law and order) Amrendra Singh Sengar told reporters.
Referring to a cut mark on the abdomen of the victim, he said that medical examination was being conducted.
"The medical examination is being conducted to ascertain several aspects. This aspect will also be looked into in further examination," Sengar said.
He said that for delay in lodging the FIR and failing to take prompt action in the matter, Kharkhauda Station House Officer Dinesh Kumar Singh has been removed from the post and sent to police lines.
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Police and Provincial Armed Constabulary (PAC) personnel have been deployed in the area to bring the situation under control.
According to Superintendent of Police (rural) Captain M S Begh, the victim's father had lodged a complaint at Kharkhauda police station against village head Nawab Khan, cleric Sallaullah, his wife and daughter Nishat for abduction and rape.
The complainant alleged that Nawab along with five others abducted his daughter on July 23 and took her to a madarsa where they raped and illegally confined her. They also forcefully made her sign some papers related to religious conversion.
He said the woman's medical examination has confirmed rape and cuts were found on her abdomen. He rejected media reports that the girl's kidney had been removed.
Meerut District Magistrate Pankaj Yadav said Sallaullah, his wife and daughter have been arrested in the matter.
Since the incident occurred in Hapur area, he said the post magisterial inquiry into the matter will be taken by Hapur District Magistrate.
A magisterial inquiry into the incident will be conducted by Deputy District Collector S P Singh, who will submit a report within a week, District Magistrate (Hapur) Rajesh Kumar Singh said.