The barrel was found abandoned near a trade union office on the shores of a backwater in Kumbalam.
Police reached the area following complaints that foul smell was emanating from the barrel reportedly recovered two months ago during a dredging operation in the backwater.
They found the skeleton in the barrel which was broke open.
Top police officials, including Police Commissioner M P Dinesh, visited the place.
Police said the skeleton had been sent to the Medical College Hospital in Kalamassery for scientific analysis.
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