The Stamp Duties Act was in existence since colonial era. The present one was first promulgated in 1990 and reviewed in 2004. In the past, attempts to enforce it have all failed. From 2004 upward, the CBN had issued 3 circulars on its enforcement without any positive result.

What Has Changed?
Much have changed. Although the law has been in place, what was lacking was the enforcement culture. Government is now determined to enforce all financial laws and regulations in order to shore up revenue and prevent leakages.
What Does It Cover:
It covers any note, memo or writing whereby any amount of money (in excess of N4.00) is acknowledged or expressed to have been received, deposited or paid.
image: http://i1.wp.com/expressng.com/wp-content/uploads/2016/01/stamp.jpg?zoom=1.5&resize=500%2C274
At the upper right of the cheque dummy, you will see the coat of arms with stamp duty paid on it
At the upper right of the cheque dummy, you will see the coat of arms with stamp duty paid on it
How Does It Affect You?
A financial transaction levy of fifty naira is deducted on any receipt via eletronic payment, cash or cheque in excess of N1000.00. Note that fifty naira is deducted NOT on every N1000.00 but on every transaction in excess of N1000.00 whether it is in millions or billions.


Are There Exemptions?
Yes. It does not include self-to-self transfer whether intra or interbank, and it also exempts transfers and withdrawals involving savings accounts that are used by majority of low income Nigerians.
Is It A Nigeria-Only Practice?
No. It is a global practice that has been in place (to varying applications) in many countries.
Benefits:
If fully enforced, the Stamp Duties Act has the potential to generate over 2 trillion naira annually of which only about 50 – 100 billion will come from the fifty naira cash receipts. The rest will come from stamp duties on shares, bonds and property purchases. It is also capable of generating between 100 000 – 300 000 jobs in the postal service subsector.
Legal Implications
Receipts not backed by duty stamps are not legally recognized and are therefore not acceptable as evidence before the courts.

Read more at http://expressng.com/2016/01/n50-stamp-duty-and-how-it-affects-every-nigerian/#O4MvJYdz1BfB73oI.99

Source - http://expressng.com/2016/01/n50-stamp-duty-and-how-it-affects-every-nigerian/

It is too much, 10 naira or 20 naira would have been fair.