The bodies were recovered near Narwana and Garhi areas of the canal. While eight bodies were recovered from Narwana, three bodies and four skulls were found from Garhi, police said.
Police said they received information yesterday that a body had been spotted in the canal when the water level was low. Later on, a search was started.
Eight bodies were recovered from the canal near Dhakal village in Narwana, a police official of the Sadar Police Station said.
"The water level in the canal was low and we found the bodies, which were in mutilated state," he said.
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"We have kept the bodies for their identification and are in touch with our counterparts in Punjab and Himachal Pradesh," the police official said.
The bodies were kept in the civil hospital at Narwana.
The Bhakra Canal enters Haryana from Punjab.