Dear Imran,
CTC is a management account formula to assess the overall cost incurred by the employer per employee per annum. Therefore, CTC would include all the costs relating to direct benefits and indirect benefits given to the employee. Statutory Contributions made by employer to EPF,ESI,Gratuity etc., in respect of employees form part of the various indirect benefits.
Hence the applicability and the calculation of statutory benefits like EPF,ESI have to be determined only on the basis of the monthly salary or wages as defined under the respective laws for the purpose and as such CTC is not a relevant factor in this regard.
I would like to request you to go through the EPF Act,1952 for further clarification in this regard.