Six months into the presidency of Mohammed Morsi, Egypt’s new constitution has granted the Egyptian Armed Forces (EAF) greater autonomy and a more formal political role than they ever enjoyed under his predecessor, Hosni Mubarak. Morsi and the Islamist majority in the Constituent Assembly may have found it expedient to agree to the EAF’s terms in order to ensure the forces’ neutrality in the current phase of the country’s democratic transition, but this will prove costly.

Mammoth tasks lie ahead for Egypt’s new, democratically elected civilian authorities. They will need to change how the state-owned commercial sector and public enterprises work in order to unlock the national economy’s potential for sustained and equitable growth. The state’s massive civilian bureaucracy desperately needs sweeping administrative reform. And the civilian authorities will have to democratize and decentralize the country’s local government structure from top to bottom.

Self-perpetuating networks of retired EAF officers extensively permeate virtually all these sectors. If this deeply entrenched “officers’ republic” is confronted with a determined reform program, its resistance to Morsi and any cabinet that is appointed under his watch will likely stiffen, potentially bringing the country to a standstill.

Indeed, the cabinet of Prime Minister Hisham Qandil has already run into resistance as it seeks to get Egypt’s state apparatus back to work. Civil servants may not be politically or ideologically opposed to Egypt’s new authorities, but their initial ambivalence is reportedly turning into go-slow tactics and passive noncooperation with government directives.