The bodies were found in between Mankara-Lakkidi railway stations near Ottapalam this morning, police said.
The three had gone missing from their homes in Konni on July 10.
A police team from Pathnamthitta and relatives of all the girls rushed to Thrissur Medical College, where the bodies were brought for inquest and postmortem.
The other girl was found with critical head injuries as well as injuries all over her body, according to hospital officials.
The deceased were identified as Athira and Raji and the seriously injured as Arya.
