Their classmate, 12-year-old Dinesh Meghwal, was beaten up last week by a teacher allegedly for touching a non-Dalit's food plate.
"I touched their plate by mistake so they beat me up. They beat me very badly," Dinesh Meghwal said.
The students from the Meghwal community say they are now being threatened by the upper caste Jats in their village - the community to which teacher belongs.
The teacher Hema Ram Jat, who was arrested after the incident last Friday, is now out on bail.
Calling for action over the incident, around 50 Dalit children from the senior secondary school from the village sat in protest outside the collector's office in Jodhpur with a memorandum.
They say discrimination is rampant in their village school where upper caste Jats are in majority. "They treat us very badly. Our plates are kept separately and that is also the reason our friend was beaten," said a classmate of Dinesh.
Dinesh's father Malaram said that after his son was beaten up, he went to the school to protest, but he too was beaten by the school teacher.
"There is pressure now on the students and the parents. The Dalit children are not going to the school. This is a matter of concern," Kishan Meghwal, a Dalit activist from the area, said.
The education department has asked for a report into the case. The police have registered a first information report and said they are investigating the matter.
"Strict action would be taken. There is no question that caste-based discrimination will be allowed," Jodhpur Superintendent of Police Pradeep Mohan Sharma said.
Rajasthan has the fifth highest number of crimes against Dalits in the country according to the National Crime Records Bureau. There has been an increase of 22 per cent in the number of crimes like these registered under the Scheduled Caste and Scheduled Tribe Act in the last one year.
Election Results for Lok Sabha Election 2019 will be out on May 23. Get the latest election news and live updates on ndtv.com/elections. Catch all the action on NDTV Live. Like us on Facebook or follow us on Twitter and Instagram for news updates from each of the 543 parliamentary seats for the election 2019