If your organisation is carrying out of loading and unloading work regularly or occasionally, it is mandatory to register your organisation under the said Act. You have mixed two things (You started with the point- have to go under medical examination- if it has to go, then do the medical check up, it does not cost more then 1500 for whole body check up or simply you can ask employee to bring fitness certificate from an MBBS doctor). All the industry mentioned in the schedule of The Maharashtra Mathadi, Hamal and Other Manual Workers (Regulation of Employment and Welfare) Act, 1969
comes under purview of the Act.
If you read section 5 of the schedule, it mention as :
5. Employment in markets, and factories and other establishments,
in connection with loading, unloading, stacking, carrying, weighing,
1 [measuring, filing, stitching, "sorting, cleaning or such other work]
including work preparatory or incidental to such operations carried on
by workers not covered by any other entries in this Schedule
So your organisation falls under this category.
I hope I have solved your query.