The case was registered at the Aluva police station here on the complaint of a woman, who is a native of Angamally, the constituency which Thettayil represents in the state assembly.
While Thettayil is the first accused in the case, his son Adarsh has been named as the second accused.
Police said the woman's statement has been noted down and she was also taken to the hospital for medical examination.
Home Minister Thiruvanchoor Radhakrishnan told reporters at Kottayam that since it was a complaint of sexual harassment, lady officer Sajita Begum Sultan, Superintendent of Police at Ernakulam Crime branch, would investigate the matter.
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Reacting on the charges made against him, Thettayil said he would face the case legally and said it was part of a 'political conspiracy' to tarnish his image.
Thettayil told television channels that he knows the woman and her family, but her complaint was 'baseless'. He said that she had approached him to get married to his son.
The case is likely to take the wind off the sails of the Left Democratic Front's agitation on the solar scam both inside and outside the assembly.
Pro-UDF activists took out marches in various parts of the state, shouting slogans against Thettayil.