This week’s landmark presidential election should end six decades of effective military rule in Egypt, but it remains unclear how much authority the generals who took over from Hosni Mubarak will cede to the elected leader.

One thing is certain, though: The generals want no interference with their budget, their economic empire or promotions.

The main question is whether a military that has grown accustomed to virtually unchallenged domination over the past six decades will be willing to quietly give it all up, or know how to deal with a civilian president if one is elected.

All of Egypt’s four presidents since the overthrow of the monarchy in a 1952 coup have come from the military. The nation’s most powerful institution, the military has over the years built a seemingly unshakable image as a bastion of patriotism and the defender of the nation.

Retired generals have consistently been given top government jobs as Cabinet ministers, ambassadors, provincial governors, chairmen of key state-owned firms or key posts in the private sector. Combined with the powers of the president, a loyal police force and a coterie of very wealthy businessmen, they have held a stranglehold on Egypt.

High on the list of their worries is whether the armed forces’ budget will be subjected to public debate in the legislature, currently dominated by Islamists, most of whom are at sharp odds with the military.

There is also the question of whether the military’s vast economic interests – giant construction companies, farms, water-bottling facilities and a nationwide chain of gas stations – would come under civilian oversight or be forced to compete for lucrative government contracts like everyone else.

Already, a member of the ruling military council has sternly warned that anyone who tries to touch the military’s economic interests would be harshly dealt with.

One more source of concern is whether the next president would have the authority to pension off top brass after they reach the retirement age of 60. Many members of the ruling military council are well into their 60s or 70s.

None of these problems publicly surfaced under Mubarak, a career air force officer who allowed the military to freely pursue economic interests and accepted counsel from his defence minister on army promotions and retirement in return for the generals’ support throughout his 29-year rule.

Confining the military’s role to the defence of the nation has been a main demand by the pro-democracy groups who engineered the anti-Mubarak uprising and later called for the military to step down. Some want the generals to be put on trial to answer for alleged crimes during their rule, including the killing of peaceful protesters, torturing detainees and putting civilians on trial before military tribunals, including icon figures from the protest movement.

Mubarak, the generals’ mentor, is on trial for his life on charges of complicity in the killing of nearly 900 protesters during the uprising, as well as corruption. The 84-year-old former president is to be sentenced on 2 June.

Perhaps with Mubarak’s ordeal in mind, the military recently won protection for all personnel, whether retired or in active service, from being put on trial in civilian courts.

Publicly, the generals say they have no wish to remain in politics and would step down immediately if they could. Any talk of wanting to hold on to power is baseless, they say.

They have not shied away from singing their own praises, but their infrequent public appearances have meant they had to rely on a powerful state media, as well as influential journalists and several loyal private television stations to promote them as the nation’s faithful sons.

But it was under the military’s watch, say critics, that Egypt has seen a surge in crime, the loss of half the country’s foreign reserves as the economy faltered and the kind of disasters thought unimaginable just a little more than a year ago – including the deaths in February of more than 70 soccer fans in a riot as police stood by and watched.

The 13 candidates contesting today and tomorrow’s election include Islamists, liberals and two with military backgrounds, among them a retired air force commander who was Mubarak’s last prime minister.

No outright winner is expected to emerge from the two-day vote, so a runoff is scheduled for 16-17 June between the two top finishers.