Baroocha and her husband Kinsely Samuel, responsible for the building plan, were arrested in Chennai and being brought here for further investigation, they said.
Police have earlier arrested one Jose, the contractor for supply of workers for the construction of the church.
Police said they were on the look out for administrators of the CSI church Manohar and Daniel and priest John Chelliah, who were absconding after the incident that occurred on the night of May 27.
Meanwhile, city Corporation Commissioner Lakshmi said the plan approval given by the corporation had been cancelled and the church authorities would have to make a fresh application with a new plan for construction.
District Collector M Karunakaran had ordered an inquiry into the incident by Assistant collector Fermi Vidhya, who will be assisted by tehsildar Indhira Gandhi.