What do you mean by separate registration? When the Factories Act and the rules framed under that Act are applicable, your establishment will be covered under the same. When you are covered under the Factories Act, your employees will automatically get the benefits of welfare, security, and health measures as provided under the Act. In addition, specific registration is not required for each worker. However, for coverage under other Acts, like the ESI Act, EPF & MP Act, etc., you have to initiate registrations separately following the respective Acts.
There is also a system of granting work permits/work cards to workers engaged in headload work within the factory in some states. This is meant only for laborers who are engaged in loading and unloading activities and to distinguish them from headload workers from outside the factory.