"Four columns of the army, numbering about 800 troopers, had been deployed in Bayana and three adjoining villages where the situation continued to be tense," T Ravi Kant, Bharatpur district official, said.
The Gujjars, an ethnic group, are demanding that they be allowed to be included among the "scheduled castes", India's socially and economically weakest communities who are granted state aid and jobs.
Currently they do not qualify for government jobs or a place at educational institutions.
The police said they were forced to open fire after teargas and rubber pellets failed to disperse the crowd.
The latest violence comes nearly a year after protests by Gujjars in Rajasthan claimed 26 lives.
Gujjar leaders said the protests would continue and spread to other areas until their demands were met.
They claimed Rajasthan's ruling Bharatiya Janata Party had promised to give them scheduled tribe status before local elections in 2003.
The state government has said such a decision can only be taken by the federal government to which it had sent a recommendation.