The woman has also accused 10 others for the forced conversion and marriage.
Kalam was produced before a local court Tuesday and sent to judicial custody.
The medical examination of the woman has been conducted and its report is awaited. The victim has also recorded her statement before the magistrate.
SHO of Meerapur police station, Kamal Singh said the woman reached the police station Monday and told the police that she has somehow escaped from Kalams house where she has been detained since September last year.
On the basis of her complaint, the police have registered a case against 11 persons, including Kalam, on various charges including rape.
The SHO said the woman belongs to Delhi and had come to Muzaffarnagar after she married a local youth in 2003. She has two children. She had joined Kalams nursing home as a paramedical staff, he added.