Fellow nuns who had gone to her room after she missed the morning mass at the chapel found 69-year-old sister Amala dead in a pool of blood in her Lisieux Carmel Convent.
A deep injury with a sharp edged weapon on her back and minor wounds were found on her forehead, police said.
Suspecting that it is a case of "unnatural death" police immediately constituted a team of officials headed by Pala DySP Suneesh Babu to probe the case.
Police suspect the incident occurred past midnight.
"It is a case of unnatural death," said Ernakulam Range IG M R Ajith Kumar after reviewing progress in the case.
The doors of her room were not locked from inside.
Sister Amala's family belongs to Ramapuram near Pala in the district. She was suffering from fever since past couple of days, her fellow sisters said.
Teams of dog squad and forensic experts were called to collect evidence. Her body was taken to Government Medical College, Kottayam, for postmortem.
The Pala diocese of the Catholic Church refused to comment citing the investigation process which was under way.
Pala is a Catholic dominated town in Kottayam in Kerala.
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