The woman was found strangled and without clothes at Kharjuna village in the district on Sunday with the husband alleging that she was raped and murdered.
Murshidabad Superintendent of Police Humayun Kabir, however, claimed that the woman had an affair with a man with whom she wanted to elope and that she was not raped.
"We have started an investigation after her husband complained that the police indulged in character assassination of his wife," commission Joint Secretary Sujay Kumar Haldar said.