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