Why does the Quartus II programmer fail to program the Encyption Key Programming file?

Description

Due to a problem in Quartus® II software, when you program the Encyption Key Programming (.ekp) file to Stratix® V, Arria® V or Cyclone® V device using Quartus II programmer, you may see following error.

Info (209005): Programming status: Detected failed attempt to program the non-volatile design security key on device 1
Error (209012): Operation failed

Resolution

To work around this problem, use the JAM™ Standard Test and Programming Language (STAPL) Format (.jam) file instead of the .ekp file to program design security key.

To generate the .jam file for design seruity key programming in Stratix V, Arria V or Cyclone V, refer to AN556: Using the Design Security Feature in Altera FPGAs (PDF). 

This problem is scheduled to be fixed in a future release of the Quartus II software.