After you file your tax return for the assessment year usually you are sent an intimation notice which clarifies on the tax refund payment to you. And this then after successful verification is credited to your account. Nonetheless, if the amount of the refund as computed by the tax department is less than Rs. 100 then it shall be adjusted in future tax filings.

Likewise, say if you have some tax refund due next year then this year's small tax refund amount will be clubbed with that and paid to you accordingly. This is in case the refund due to you in the following year is more than Rs. 100 else if you have to pay taxes then the net amount after adjusting for the small refund amount shall have to be paid by you.
As and when the income tax return is filed and verified by you the tax department at its end processes the same and on successful process it issues an intimation notice u/s 143(1) which specified on the tax amount due or refund i.e. payable to you.
Small tax dues have to be cleared by taxpayers
Unlike, the refund amount, in case a small tax becomes due to a taxpayer then he or she needs to clear the same before filing the ITR. Importantly, in a press note in 2012, "the demands of less than Rs 100 would not be enforced but liable for adjustment against future income tax refunds. Practically, it has been seen that income tax refund amount of less than Rs 100 is not processed and credited into individual's bank account by income tax department."
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