He was moved to a police camp on Sunday morning, officials reported.
Police stated that a third sexual assault case has been recorded against the Palakkad MLA following a complaint lodged by a resident of Pathanamthitta district.
The Special Investigation Team (SIT), already investigating two other similar cases against him, has been assigned to look into this latest case, sources disclosed.
Mamkootathil, who had been residing at a hotel in Palakkad, was taken into custody at midnight and transported to Pathanamthitta.
Authorities have indicated that his formal arrest is expected to occur later.
The Kerala High Court had earlier provided Mamkootathil with interim protection from arrest concerning the first case, which involves allegations of rape and coercing a woman into having an abortion.
In the second case, a sessions court in Thiruvananthapuram granted him anticipatory bail.
Following these allegations, the Congress party expelled Mamkootathil.
