The new decree from Egypt’s military rulers means the incoming civilian president will have very limited powers.

Egypt’s ruling Supreme Council of the Armed Forces has issued a new constitutional declaration granting itself near total autonomy in military matters and the ability to exercise a de facto veto over the drafting of a new constitution, all as Egypt awaits its first president since an uprising ousted Hosni Mubarak.

The declaration, which contains eight amendments to an earlier text decreed by the SCAF in March 2011, was printed in the state’s Official Gazette on Sunday, giving it the force of law, and was announced by state media, minutes after polls closed at the end of two days of voting.

The Muslim Brotherhood, whose candidate, Mohammed Morsi, is leading unofficial vote counting, rejected the declaration. Human rights activists also expressed immediate concern. Human Rights Watch researcher Heba Morayef tweeted that the new amendments had rendered the military’s promise to hand over power by June 30 “meaningless,” while Hossam Bahgat of the Egyptian Initiative for Personal Rights wrote that Egypt had “completed its full transition into a military dictatorship”.

In several respects, the declaration resembled a document drawn up late last year by Deputy Prime Minister Ali al-Selmi, a member of the military-approved cabinet who had been tasked with creating a set of “supraconstitutional” principles that would have guided the creation of Egypt’s new founding document.

The Brotherhood, confident in parliamentary gains, accused the military of trying to shut Islamists out of the process, and the Selmi Document, as it was known, went down under public protests. It would have shielded military affairs from scrutiny and also given the SCAF a veto over the constitution.

That, it appears, is exactly what Sunday night’s new declaration does.

‘A constitutional obscenity’

Most prominently, the declaration gives the military total power to oversee its own affairs, removing the president’s role as commander-in-chief. The head of the SCAF, former Mubarak-era defence minister and Field Marshal Hussein Tantawi, assumes that power.

The president is allowed to declare war only with the SCAF’s approval, and only the SCAF chooses its leaders.

The result, analyst Issandr El Amrani tweeted, is that Egypt’s separation of powers had been drastically altered, with the military turned into “a constitutionally separate institution alongside the executive, legislative and judiciary”.

The SCAF also placed itself astride the process of drafting Egypt’s new constitution.

The 100-member assembly of parliamentarians, religious scholars, legal experts, youth activists, and trade union representatives tasked with writing the document will now be subject to a de facto veto.

If Tantawi, the president, the prime minister or the head of the judiciary object to any article in the constitution draft and the assembly fails to find a solution, the article can then be referred to Egypt’s Supreme Constitutional Court for a final judgment.

Objections can be made if any article “conflict[s] with the revolution’s goals and its main principles or which conflict with any principal agreed upon in all of Egypt’s former constitutions,” according to the declaration.

This means that a court stacked with judges appointed by Mubarak and which has already ordered parliament dissolved will have the power to decide what belongs in the new constitution.

“Giving the constitutional court a binding veto over any constitutional provision with only the vaguest guidance on the standards to use is simply a constitutional obscenity,” wrote legal scholar Nathan Brown on the Arabist, Amrani’s website.

The SCAF also arranged a back-up option that could bring the process even more directly under its control. If the assembly encounters any “obstacle” that prevents it from working, the SCAF itself will choose an entirely new assembly. Since some members of the assembly already withdrew days ago, this is a real possibility.

The declaration also continues the battle between the SCAF and the Brotherhood over parliament, which the supreme court ordered dissolved on electoral procedural grounds on Thursday – a ruling the Brotherhood has rejected. SCAF, apparently pushing its view that the current parliament is finished – provides for new parliamentary elections to be held one month from the date a new constitution is approved by national referendum.

Since the country cannot elect a new parliament until a new constitution is approved, there would be pressure not to stall the process. With no parliament, the president will take his oath of office before the supreme court, the document says.

The declaration specifies that the military will assume legislative responsibilities until a new parliament is elected. It also enshrines the military’s right to put down “internal unrest” if the president requests it. Recently, the justice ministry issued an order granting the military power to arrest civilians, something it had been doing unofficially since the uprising.

Despite the assumption of huge powers, SCAF’s declaration also leaves responsibilities with the president. He will still choose his vice presidents and cabinet and propose the state budget, as well as propose laws and issue pardons. The president will also sit at the head of a new National Security Council “tasked with evaluating affairs concerned with means of securing the country and its safety,” but the power of that council appears to be nominal compared to the SCAF.