Similar question was asked earlier at this link:
https://www.citehr.com/279601-please...ts-during.html
Coming back to the question asked. Should PF be deducted from salary of such interns/probationers etc. or not? Ideally speaking NO. But Practically speaking YES.
See. Ideally, such persons can't be in any manner termed as employee of the company because then the distinction just vanishes away. Its with the belief that in future if their performance is found satisfactory then such personnels will be subsumed as an employee and then only exclusive employee benefits should be made available to him.
But wait. What legislation lays down is a term "Excluded employee" and through that a person earning below Rs 6500 is not to be covered under PF. Clearly engineers will be paid much higher than this Rs 6500 a month so this door stands closed. If we go by the intent of the legislation then we must deduct PF as been held by SC too in Andhra University v. R.P.F.C (1985) in line with the preamble of the legislation.
Now lets see practical aspect of this. You got already 1000+ employees meaning thereby good size company. For deducting additional PF for 3 trainees won't make a difference. But you won't be having anything to prove if Inspector visits your office and questions such non deduction. The cost of non-deduction will be far more than cost of deducting as in any case he won't be submitting like that and then you must have good legal team and then case to go to tribunal or something. Is it even worth it? Plus, we all know that nomenclature of trainee etc. is only for distinguishing probations, notice period, increment, termination periods. Not in work sense at all. So lets see the way legislation wants us too and reduce the confusion and resulting impact on us.