The Apollo Hospitals contended that the probe panel is going beyond its terms of reference.
Jayalalithaa was in Apollo Hospitals here for 75 days in 2016 before she died there due to cardiac arrest on December 5, 2016.
The Apollo Hospitals has also filed a petition in the high court to appoint an independent medical board, if the Commission's terms of reference also cover an inquiry into the treatment given to Jayalalithaa.
In an order issued detailing the terms of reference of the inquiry commission, the Tamil Nadu government had said it would "inquire into the circumstances and situation leading to the hospitalisation" of Jayalalithaa on September 22, 2016 and "subsequent treatment provided till her unfortunate demise" on December 5 that year.
Ever since Jayalalithaa's death, there have been allegations of foul play.