The girl also alleged that rape and molestation of inmates have been going on in the orphanage at Silapathar for long, but a section of the local people said the director is being framed.
The 13-year-old girl lodged a complaint with the police that the director forcefully took her out of her room and molested her in another room on the night of January 7.
After the FIR was lodged on January 8, the director was arrested and forwarded to judicial custody, district Superintendent of Police Nilesh Sawakare said.
The girl said in the FIR that she had managed to escape from the orphanage and took shelter in a neighbour's house.
Official sources said the orphanage sheltering around 100 orphans and destitute is funded by the Assam Social Welfare and Social Justice department.
"Rape and molestation of the inmates are going on for a long time and she somehow managed to escape to expose it," the girl alleged before the media.
Some local organisations have also filed a separate FIR alleging illegal activities in the orphanage.
A group of women also demonstrated before Silapathar police station yesterday demanding arrest of its director.
However, a section of the local people claimed he is being framed by certain quarters as the orphanage has been operating successfully.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)