The order was issued by Justice P Bhavadasan on a petition by Thettayil seeking to quash the FIR registered against him in the case.
The court also issued notice to the complainant and said she would be heard on Thursday.
The Judge observed that prima facie no offence is disclosed in the complaint against Thettayil.
Thettayil, JD-S MLA from Angamally, is the first accused in the case while his son, Adarsh, is the second accused.
Aluva Police had on June 22 registered a case against Thettayil and his son for sexual harassment based on the complaint of a woman that she had been sexually harassed by the father and son.
"It is reliably understood that the woman had been instigated by some prominent leaders of the ruling political Front to fabricate a false case and to file a frivolous complaint against the petitioner and his son with the ulterior motive to tide over the political crisis prevailing in the state," the plea had stated said.
"The inordinate delay in preferring the complaint is a tell tale circumstance buttressing the above suspicion. Still the police even without ascertaining the veracity of the allegations registered the crime on extraneous considerations," the petitioner submitted.
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