Police said the mishap occurred when the seer, Punyananda Valmiki Swamiji of Rajanahalli (41), and his junior, Basavaraj (13), were returning to Davanagere from Karur in Harihara taluk.
The van driver was admitted to a private hospital here and his condition was stated to be critical.
Irked by the incident, the public gathered near the spot and put boulders on the track. The agitators, demanding building an overbridge at the spot, removed pendrol clips for half a kilometre stretch on the Bangalore-Hubli sector, bringing rail traffic to a halt.
Police resorted to lathicharge to control the agitators and Karnataka State Reserve Police force was rushed to the spot.
Following the protest, Bangalore-Hubli fast passenger was detained at Davanagere, Hubli-Kochuveli Express halted at Haveri near Hubli, Dadar-Yesvantpur Express held at Harihara station and Bangalore-Dharwad Express detained at Chickjajur.
South Western Railway authorities said it would take two to four hours to replace the clips and resume the services.
The last rites of the Swamiji would take place at Rajanahalli village tomorrow.