Crime Branch sources said the charge, outraging modesty of a woman, was present in the complaint filed by the woman who had alleged she had been sexually harassed by Thettayil and his son.
The sources said she had clearly stated that she had been molested. However, local police had not added the section.
The fresh charge was filed before the Aluva Magistrate court, the sources said, adding that IPC section 34 (Common Intention) had been deleted from the list of charges.
The complainant's counsel also sought time for filing statement.
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The court had earlier this week stayed for 10 days further proceedings against Thettayil and had observed that prima facie, no offence was disclosed in the complaint against him.
Thettayil, JD-S MLA from Angamally, is the first accused in the case while his son, Adarsh, is the second accused.
Aluva Police had recently registered a case against him and his son for sexual harassment based on the complaint of the woman that she had been sexually harassed by the duo.