Late fees is mentioned in Section 47(2) of the Act, i.e
Section 47(2):- Any registered person who fails to furnish the return required under section 44 by the due date shall be liable to pay a late fee of one hundred rupees for every day during which such failure continues subject to a maximum amount calculated at a quarter percent of his turnover in the state or union territory.
Hence for GSTR-9 the Late fees both under SGST and CGST is Rs. 200 per day subject to the maximum as mentioned above.
There is No late fee for delayed filling of GSTR-9C and further there is no specific penalty for GSTR-9C in the GST Act. However it may be serve by General Penalty Section 125.ie
Section 125:-Any person, who contravenes any of the provisions of this Act or any rules made thereunder for which no penalty is separately provided for in this Act, shall be liable to a penalty which may extend to twenty-five thousand rupees.
The penalty under section 125 is not a mandatory penalty and the amount is not fixed because it may extend to Rs. 25000.00 i.e. from Re.1 to 25000.00