A clash broke out after police tried to stop followers from visiting Kerala's Kurisumala, a pilgrimage centre under the Neyyattinkara Latin Catholic Diocese.
Hundreds of people who joined the protest demanded a new cross to be erected at Kurisumala in Bonacaud near Vithura.
The earlier cross erected there was damaged in November 2017.
"The followers refused to disperse and hurled stones at them, following which the police resorted to lathi charge. The crowd had also destroyed the barricades," police said.
"Several others, including police personnel, have also been injured in stone pelting and lathi charge," police added.
Following the incident, visitors have been banned from entering the pilgrimage centre for the time being.