An income taxpayer is liable to pay late ITR filing fees of Rs 5,000 if the tax return is filed after the deadline but on or before December 31 of the relevant assessment year. And Rs 10,000 if tax return is filed after December 31 but before the end of the relevant assessment year, i.e., before March 31. If you are a small taxpayer whose gross total income does not exceed Rs 5 lakh then the maximum fees you are liable to pay is Rs 1,000.