The incident came to light during a routine inspection of the school by women staff of the Mukherjee Nagar police station, a senior police officer said.
The accused, Awadhesh Prajapati, taught at Sarvodaya school under the Delhi government, and two cases were registered against him, the officer said.
He has been arrested and sent to judicial custody, the officer said.
"Seven students had already made complaint about the teacher, while five more came forward today narrating their ordeal," the officer, who did not wish to be named, said.
The girls later shared their trauma with their teachers as well as parents on Friday and the matter was reported to the police.