Egyptian troops have been seen gearing up for unarmed combat as the clocked continued to tick on the 48-hour ultimatum handed to President Mohamed Morsi.

Images from Al Jazeera's Egypt news channel satellite showed Egyptian troops chanting, marching and training for unarmed combat in the streets of the Red Sea city of Suez at the mouth of the Suez Canal on Tuesday.

Security sources in Suez said that forces from the locally based Third Field Army strengthened their presence in the city overnight after the clashes. Armed vehicles were also sent on patrol, the sources told Reuters.

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Military sources said on Tuesday that troops were preparing to deploy on the streets of Cairo and other cities if necessary to prevent clashes between rival political factions.

The UN have now stepped in to urge Egyptian president Morsi to engage in serious national dialogue" with the people, as the military warned of a possible coup if he does not respond within 48-hours.

Rupert Colville, spokesman of UN High Commissioner for Human Rights Navi Pillay, also said the role of the military, which gave Mursi a 48-hour ultimatum on Monday to resolve the impasse after mass anti-government protests, was crucial.

“We call on the president of Egypt to listen to the demands and wishes of the Egyptian people expressed during these huge protests over the past few days, and to address key issues raised by the opposition and by civil society in recent months,” he told a news briefing in Geneva.

In a statement issued at 2am on Tuesday morning by President Morsi's office, Egypt's leader rebuffed the army's 48-hour deadline to meet the demands of the people, despite warnings that they would mount a military coup.

Nine hours after General Abdel Fattah al-Sisi delighted Morsi's opponents by effectively ordering the president to heed the demands of demonstrators, the president's office said that he had not been consulted and would pursue his own plans for national reconciliation.

“The president of the republic was not consulted about the statement issued by the armed forces,” it said. “The presidency sees that some of the statements in it carry meanings that could cause confusion in the complex national environment.”

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The statement continued: “The presidency confirms that it is going forward on its previously plotted path to promote comprehensive national reconciliation ... regardless of any statements that deepen divisions between citizens.”

Describing civilian rule as a great gain from the revolution of 2011, Egypt's first freely elected leader, in office for just a year, said he would not let the clock be turned back.

Since this statement was released two spokesmen for the president have quit, according to a foreign ministry official, on top of six cabinet members who resigned yesterday.

But in highlighting that his plans for reconciliation remain the same as those he had spelt out before, he was speaking of offers that have already been rejected by the opposition, leaving it improbable that such compromises would bear fruit before Sisi's deadline.

Morsi also spoke to US President Barack Obama by phone on Monday, the presidency said in a separate statement. Morsi stressed that Egypt was moving forward with a peaceful democratic transition based on the law and constitution, it said.

On Monday the Egyptian military had issued a stark warning that it would be prepared to mount a coup against the Muslim Brotherhood, setting a 48-hour deadline for the government and its opponents to solve the growing political crisis or face military intervention.

Speaking in a televised address, as thousands of anti-government protesters turned out across the country for a second day, General Abdel Fattah al-Sisi warned that the military would offer its own “road map for the future” unless a consensus was reached.

On Monday, Egypt’s commander-in-chief praised anti-government demonstrations on Sunday, in which millions of Egyptians took part, as an “unprecedented” and “glorious” expression of the popular will. “If the demands of the people are not realised within the defined period,” he had said, “it will be incumbent upon [the armed forces] ... to announce a road map for the future.”

Soon afterwards, five military helicopters flew in formation over Tahrir Square – the cradle of the country’s 2011 Arab Spring revolt – with Egyptian flags tasselled to the fuselage. The jingoistic display was met with roars from the crowd below.

Mahmoud Badr, founder of the coalition which has spearheaded the renewed anti-government revolt, welcomed the army’s intervention as a move towards early elections.

“The statement of the armed forces has a single idea – supporting the will of the Egyptian people at this moment, which means early presidential elections.”

Many who heeded the call to revolt are happy to contemplate the military toppling Egypt’s elected President.

“After the past two and a half years, there is no other option than having the military as a sponsor,” said Mamdouh Badr, an Egyptian activist. “Egypt now has serious problems. We need the military as a solid structure to be part of the political scene for the next four or five years.”

However, many other Egyptians, recalling the street protests which demanded an end to the period of martial rule following former President Hosni Mubarak’s ousting in 2011, reacted with disbelief and apprehension to the growing clamour for a military coup.

“The military are Mubarak’s men through and through,” said Farah Saafan, a Cairo-based journalist. “I don’t see why we should trust them. They committed horrible atrocities when they held power and should be held accountable for it.”

Monday's gambit by Egypt’s generals turned the screw ever more tightly on Mr Morsi. He is now facing increasing pressure on several fronts.

The state news agency announced yesterday that five cabinet ministers were tendering their resignations in solidarity with the anti-government protests. Meanwhile the coalition behind this week’s massive demonstrations issued its own ultimatum to Mr Morsi, telling the President he must stand down on Tuesday.

The so-called Rebellion campaign gave Egypt’s leader until 5pm to resign and trigger fresh presidential elections. If he failed to do so, it warned, organisers would initiate a wave of “complete civil disobedience”.

The developments came following a night of deadly violence outside the Muslim Brotherhood’s national headquarters in Cairo. Sixteen people are believed to have died in the protests since Sunday.

Although Sunday’s marches in the capital were largely peaceful, gun battles erupted soon after nightfall in Moqattam, the limestone cliff plateau in eastern Cairo which houses the Brotherhood’s central office. Brotherhood members who had been under attack inside the premises were eventually forced out by their assailants, fleeing early yesterday morning. Dozens of looters then broke in to the smouldering and shattered building, making off with chairs, books, sinks and air conditioning units. By midday, the national headquarters of Egypt’s governing movement had been stripped of virtually everything inside – including photos of the embattled president.

Among some of the local onlookers, there was not much sympathy for the party.

“I don’t mind the looting,” said 56-year-old Faten Shenawy. “This country is broken. I don’t want the Muslim Brotherhood.”

Speaking to The Independent, an angry Brotherhood official warned that colleagues were now discussing how they would respond. “This cannot continue,” said Gehad el-Haddad. “If it was any other party except the Muslim Brotherhood they would probably retaliate”.

There were questions about the roles of the police and the army during the incident. Mr Haddad said both were called several times but failed to respond. There was also no sign of any security presence when the looting began, despite the presence of TV crews and reporters.

Police officers have grown increasingly hostile towards the Brotherhood since the election last year.

The Interior Ministry openly warned it would not protect the group’s headquarters, while some demonstrators have adopted the iconic revolutionary chant to pledge that “the police and people are on one hand” – much to the bemusement of activists who recall the bloody battles once fought against them.

The current wave of mass demonstrations have been largely peaceful, although campaigners reported more than 40 sexual assaults by gangs against women in Cairo.