An emergency meeting has been called by the Railways in the Kota division, with the protesters refusing to move from the tracks.
Apart from the Rajdhanis, some of the other trains affected included a Shatabdi from Kota to Delhi's Nizamuddin, the Awadh Express from Gorakhpur to Bandra, the Janta Express from Bombay to Bhojpur and the Dehradun Express from Mumbai to Dehradun.
On Thursday evening, the Gujjar Reservation front of Rajasthan had called for a 'mahapanchayat' or big meeting in Samogar village of Bharatpur. They later trooped down to the rail tracks and sat there in protest.
Rajasthan Chief Minister Vasundhara Raje has said, "We are always open to discussion but this issue is now in court."
The Gujjars have launched two violent agitations blocking railway tracks and roads in Rajasthan earlier, throwing law and order out of gear.