"There have been allegations of excess and wasteful expenditure and deficiency in the standards of new Secretariat building," Governor S S Barnala said in his address to the legislative assembly session, outlining the policies of the new AIADMK regime.
The commission, headed by a retired High court judge, would "inquire into the alleged irregularities like excess expenditure, inordinate delay and deficiency in standards of construction," he said.
"Further works would be stopped to facilitate inquiry," he said.
The DMK government had held the last session in the new Assembly-Secretariat complex, a pet project of Karunanidhi, whose estimates have touched around Rs 1,000 crore.
Jayalalithaa had earlier flayed the lack of aesthetic appeal and the design of the new complex describing it as a "circus tent".
She had justified the decision to stick to the historic 17th century Fort St George building citing administrative considerations and denied any political bias.