When you are earning a salary, your gross salary will be considered as income. For example, if your gross salary is Rs. 50,000 per month and your Basic Salary is Rs. 20,000 on which PF deductions are Rs. 2,400, income tax should be calculated on the gross salary. They should deduct IT on Rs. 50,000. However, the employer will deduct only on Rs. 47,600 since your PF amount is exempted from IT (as it is a retiral benefit). But when you withdraw before retirement, that amount will be considered as normal income; hence, TDS will be applicable on the withdrawal.
In case you do not fall under the 30% IT slab, you can claim a refund from the IT department by submitting your IT returns with the help of the TDS certificate (issued by the PF trust) and Form-16.
Regards,
Ramanjaneya Reddy.G.K