The arrested were identified as V K Biju (38), personal staff of the Minister, and his friend Shamsuddin (29).
Biju was suspended from the service in the wake of the incident, an official in the Minister's office said.
Body of the 49-year-old victim, who was said to be missing since February 5, was found in a pond at Chulliyot near here yesterday, police said.
The relatives of the woman had earlier lodged a complaint with the police that she had not returned from her work place.
Biju told police that the woman had threatened him that she would disclose his alleged affair with a lady which prompted him to kill her.
Meanwhile, reacting to the incident, Aryadan Muhammed said he would not protect the culprits and they should be punished.
The minister also said he was ready for any probe to bring the truth behind the incident.
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