Mohammed Morsy, Egypt’s Muslim Brotherhood aligned president, is on a collision course with the army, or so say the headlines. But there are powerful voices within the new leadership saying there are limits to how fast the military can be sent back to barracks.

No one in the Brotherhood is suggesting that the army be dispossessed of its economic and industrial empire. Nor will there be any immediate move to deprive the General Intelligence Service of its most important responsibility – keeping the uneasy peace with Israel.

The GIS are the people who arrange prisoner swaps and ceasefires between Hamas and Israel, or reconciliation talks between Fatah and Hamas. General Omar Suleiman, the recently deceased former chief of General Intelligence, was Hosni Mubarak’s contact man with Israel.

The source for this revelation is a primary one: Khairat El-Shater, a self-made millionaire and Muslim Brotherhood financier who denies he seeks high office for himself.

‘We recognise that Mubarak succeeded in making Islamists a scapegoat for the West and that our image is negative,’ he said in an interview in Cairo. ‘We realize that we need more effort, more dialogue to explain who we are and to build confidence between us and others outside Egypt.

‘Bridges of confidence cannot be built on the basis of talks only. There must be practical solutions. We realize that at this stage we should continue to employ the same individuals who followed relations with external parties, including Egyptian General Intelligence, which held the foreign relation file with Israel.

‘This is sensitive for us, but … we have no objection for these parties to continue running these files in consultation with the president and the prime minister. We don’t want change for change’s sake. We realize that politics is the art of the possible.’

Morsy has now embarked on what could prove to be a long campaign of attrition to repatriate the powers of the presidency, which were taken from the office in a decree issued by the Supreme Council of the Armed Forces (SCAF) two days before voting began in the presidential election. He has so far acted boldly, issuing a decree reinstating parliament that was rendered inquorate by the constitutional court and then dissolved by SCAF.

Insiders say his next target will be the National Defence Council, a body which is mentioned in both the 1956 and 1971 constitutions, but which is only supposed to convene in times of national emergency. SCAF’s decree packed the body with an in-built military majority. It turned the council into a Burmese style junta.

Taking it on is a high-risk strategy. It could provoke a fully fledged military coup. But the Brotherhood is determined to establish a presidency with real powers. With the exception of the post of Defence Minister, all the cabinet appointments, they insist will be theirs.

El-Shater has the reputation, rightly or wrongly, as a hardliner in the Brotherhood, a man who combines the strengths of a strategist with the practical grip of an accountant. He controls where the money goes. He reviewed the gas contract with Israel which the transitional government in Egypt cancelled.

While he says that Egypt under new management will respect international treaties, such as the Camp David accords with Israel, he also reminds us that Anwar Sadat did not just put the peace accord with Israel through the National Assembly. He also put it to a referendum. The same thing, El-Shater implies, could happen in reverse. El-Shater has developed a working relationship with Anne Patterson, the US Ambassador, a career diplomat who has been through the mill of Islamist politics in Pakistan. The British, French and Australian and Japanese Ambassadors are regular callers. ‘These countries were 100 per cent afraid of us at the start of the revolution. Now their concerns are about 80 per cent,’ he said with a smile.

The message he gives them is the same: Morsy’s first task as President will be to establish the presidency as a national institution shared out among all political parties, with vice-presidents and their advisers representing the broadest coalition of secular politicians, Christian Copts and women. The Prime Minister will run a technocratic government, where competence not affiliation will be the test.

His second message is that the battle with the military is a distraction from the real problem facing Egypt – poverty. ‘We have huge problems. Forty per cent of our people are below the poverty line, our internal and external debt has reached unprecedented levels. All the studies say it will take several years to save Egypt from drowning.

‘If we don’t solve these economic problems, in the coming years, there may be a revolution of the hungry. If this happened in Egypt, nobody would control it. It could plunge this country into a state similar to Somalia and it would infect the neighbouring countries.’

Morsy has a mammoth task, and he has to deliver quickly.