Egypt is suffering under worse conditions now that under the dictatorship of Hosni Mubarak, Mohamed ElBaradei has told the Guardian, and it is on the brink of allowing a "new emperor" to establish total domination over the country.

In a withering assessment of the Muslim Brotherhood movement, which dominated the now-defunct new parliamentary assembly and whose presidential candidate, Mohamed Morsi, will face a run-off against Mubarak's last prime minister in elections this weekend, ElBaradei said that political Islamists had tried to take "the whole cake" for themselves following the overthrow of Mubarak last February, and as a result Egypt's ruling generals had been able to engineer an assault on the revolution.

"We are in a total mess, a confused process that – assuming good intentions – has led us nowhere except the place we were at 18 months ago, but under even more adverse conditions," said the Nobel laureate, who withdrew from the presidential race earlier this year arguing that a fair vote could not be held while the country remained in the grip of a military junta. "We are going to elect a president in the next couple of days without a constitution and without a parliament. He will be a new emperor, holding both legislative and executive authority and with the right to enact laws and even amend the constitution as he sees fit."

On Thursday two hasty constitutional court decisions by Mubarak-appointed judges appeared to strike a hammer blow at the revolution, in effect dissolving the democratically elected parliament and overturning a law that would have barred members of the old regime from running for high office. The rulings came less than two days after the Ministry of Justice extended the powers of the Supreme Council of Armed Forces (Scaf) and its soldiers to arrest and investigate civilians, a move which Amnesty International labelled as "the legal sanctioning of abuse".

ElBaradei, a former UN nuclear weapons chief turned prominent Egyptian dissident, predicted that Ahmed Shafiq – Mubarak's last prime minister and the man seen by many as a blatant embodiment of the old regime – would emerge victorious from the looming poll. "Shafiq as president of the 'new Egypt' is an oxymoron," said the 69-year-old. "In this scenario the new president would be backed by Scaf and political authority in the country will continue to be held by Scaf, but I think it most likely that he is the one that is going to win."

ElBaradei confirmed he would not be casting a vote but refused to formally endorse the growing boycott campaign – because, he argued, the failure to turn it into a mass movement could hand a propaganda boost to the regime.

At times ElBaradei has been viewed as an opposition figurehead who occupied the rare position of being able to command respect from revolutionaries, secular liberals and political Islamists. On Friday, though, he spoke out against a catalogue of revolutionary mismanagement on all sides, with his harshest words reserved for the Muslim Brotherhood – whose role in the past year's "transition process" has led many pro-change activists to blame political Islamists for empowering the military and being sucked into an electoral game designed to give the old regime a facade of democratic legitimacy.

Scared

"The Brotherhood have not served themselves well — they have scared people right, left and centre with some of the extremist views put forward from them and other Islamist groups," claimed ElBaradei.

"The Brotherhood should have realised that the vote they got at the parliamentary elections was not a true reflection of their support in the street – it was the product of a specific set of political conditions at the time. They should have reached out to other segments of society and built a broad coalition but they haven't done that – they started by saying we want to be part of big cake but they ended up wanting to have the whole cake for themselves. And that created a backlash, which will be visible in the next couple of days. People have called on them to withdraw from the presidential race, but they insist on going forward – why?"

He also argued that revolutionary momentum had been stalled by the failure of young protesters to embrace institutional leadership – wading into a thorny debate over the relative merits of horizontal and "leaderless" political change about which many activists feel strongly.

"The mortal mistake was that from day one the youth never agreed on a unified demand and never agreed to delegate authority to a group of people to speak on their behalf," said ElBaradei. "They were very happy, and we understand that, to say the revolution is leaderless and that every one of us is the revolution. But they ended up being crushed by [armoured personnel carriers] and massacred at [the TV building] Maspero.

"I hope that they have learned the lesson and I think people are now talking about getting organised under a unified leadership and engaging the new president to find a way of working together, preparing themselves for future elections and push for national reconciliation."

The call on young radicals to engage with the new president – particularly if it is Shafiq – is likely to be ignored by many revolutionaries, some of whom believe the only solution is to return to mobilisation on the street. But ElBaradei said that the broader population was fatigued with violent clashes and insisted that a process of national reconciliation was necessary to drive the revolution forward.

"Not co-operating with the new president and saying he has no legitimacy will be difficult because he will have been selected by ballot," he said. "Either we try that or we have to get into a process of national reconciliation, where people say 'well this isn't what we wanted, the process has been screwed, but for the sake of the country we need to find a formula to coexist together'. It's the question the revolution will face in the next few weeks.

"People are tired," he continued. "I'm not sure street protests will get a lot of support from the rank and file after the elections – people want so-called stability. I think we need national reconciliation for the sake of the people in whose interests the revolution was staged – the 50% of Egyptians who are below the poverty line and who have seen nothing good coming out of the revolution. In fact, for them things have got worse."