The district administration has ordered an inquiry into the incident.
"Initial information suggests that the girl was not expelled by the school but was given the transfer certificate on her brother's request," Latur district collector G Shrikant told PTI.
"I have called the headmaster of the school to find out details," the IAS officer said. The district administration is investigating the allegations made against the school, he added.
On July 19, the girl's brother went to the school and asked for a transfer certificate and the school handed over the certificate to him the next day, an official said.
The army man, who has not yet been arrested, allegedly raped the minor girl in April after promising to marry her, the official said.
The girl has claimed that the school expelled her saying its reputation would be tarnished if she continued to study there.
An offence of rape was registered in August and nine persons have been arrested in the case, Police Inspector Deepak Shinde of Devani Police Station said.
Deputy SP of Nilanga GG Ranjankar said the girl and the army man are from the same 'Laman' community and the same locality.
Meanwhile, the Maharashtra State Commission for Women chairperson Vijaya Rahatkar today asked Latur Superintendent of Police Shivaji Rathod to submit a 'factual report' in the case.