You can override the system-calculated Income Tax by manually entering the tax amount.

Go to, Run Payroll >> Run Payroll >> click on Override Income Tax

Search and select the employee

Enter the Income Tax amount which needs to be overridden and 

Click on "Save"

You can also Override the Income Tax amount in bulk by clicking on 'Import list to override Income Tax' 

Download the tax update template

Update the amount and import

Note: Override Income Tax will work only if Income Tax Computation is chosen as 'Compute for this month’ OR ‘Use previous month's TDS’ options.