The girls, both aged, eight years, had reportedly fainted after returning from their school, Sri Rahula Vidyalaya, Yaya Ata in Rajanganaya on November 10.
They were admitted to hospital and a complaint lodged on the following day with Rajanganaya Police.
A third girl, aged seven years, in a statement to the police, has denied being injected with vaccine, and that she had seen an elderly man injecting the other two girls with vaccine.
The two girls have claimed that at school, two female nurses in white had caught them and injected them with a vaccine which they had brought in a shopping bag.
A piece of cotton said to have been used to stop bleeding after the vaccination was tested by GINTC, which reported there was no trace of blood in it.
Police believe someone had scared the girls with a syringe without the needle, in order to inconvenience the principal of the school.