Rajan Gajbhiye and Shailesh Ramteke were arrested in Nagpur last night. Upon their interrogation, another teacher, Sandeep Ladkhedkar, was arrested from here.
They were remanded in four-day police custody by the local court, police said.
All of them have been suspended by the Deputy Commissioner of Navodaya Vidyalaya Committee, Pune.
At least 49 schoolgirls have lodged complaint of sexual harassment against them.
The accused have been booked under section 354 (outraging the modesty of woman) of the IPC and also under the (POCSO) Protection of Children from Sexual Offences Act.
The matter is being investigated, said Pravin Munde, Deputy Superintendent of police.