As per the recently inserted section 234F of the Income Tax Act 1961, If the total income of the assessee (after all deductions) is less than or equal to Rs 5 Lakhs, then fee liable to be paid shall be upto Rs 1000.
See, application of Section 234F depends on whether you are mandatorily required to file return or not.
If you fulfill any of the below mentioned conditions, then you are mandatorily required to file return:
1.) If the gross total income (before all deductions) exceeds Rs 2.5L/3L/5L as the case may be; or
2.) If you are a beneficiary of any asset located outside India or hold any asset (including financial interest) in any entity located outside India or have signing authority in any account located outside India as a beneficial owner or otherwise
So, in your case, If your gross income was more than Rs 2.5 Lakhs but after deductions under section 80C to 80U, it got reduced below 2 Lakhs, then you are mandatorily required to file return before due date and so Sec 234F fee shall be levied if you file return after the due date
However if your taxable income before any deduction itself is below Rs 2.5 Lakhs, then no fee shall be levied even if you file belated return.