So IDSE, which began as a small part of the MES to make up for the shortfall of uniformed engineer officers, is now asserting ownership over MES, and trying to make it independent from uniformed control. The purpose behind this is clear – such a move would free them from accountability to the armed forces. Senior commanders would then no longer be able to enforce quality of service that is desired from such an organisation.
Not mentioned in the letter, but as an obvious fallout it would mean that senior clerical staff from the forces posted to headquarters would be working under much junior civilian superintendents. Although the attempted downgradation has no direct impact on pay and allowances, it’s yet another attempt at placing the interests of a cadre over those of the very organisation it was created to serve.
(SOURCE - OP INDIA BLOG - http://www.opindia.com/2016/10/armed-forces-vs-civil-services-when-the-tail-wags-the-dog/ )