The matter is a clerical error and can be rectified.
People get payment of last financial year in next financial year due to various reasons.
company has to apply its mind to it and show the minor will to clear such errors,unless they are avoiding to make payment and reduce their expenses.
2. If the company really wants to pay you back than they could repay you back as short paid or back pay and nothing to do with tax submission.
3. Always talk to your HR to get details of your entitlements and be aware for changes in your organisation particularly when involving income and deduction.
Like other members pointed out, it surely is possible to pay what's due to you.
However, adopt an approach that's NOT like you pointing fingers @ your bosses.......DON'T let it shift to any ego issues.
Given that they are OK to correct the mistake from April, 2015, looks like there is no intent to skip the past payments. But the reason they gave....IT filings done....doesn't look logical. Quite possible they didn't apply their minds to the issue....from their point of view, it could be a minor issue.
Meet the senior Manager OR the Finance guys.....one way is to make the payment as a one-time payment this year OR as arrears for the past year.
Where there is a will, there's a way.
BTW, what's the amount involved?
All the Best.