Egyptian policy regarding Israel these days is a troubling indication of the instability in the country. The Supreme Council of the Armed Forces is on a collision course with the new political forces and particularly the Muslim Brothers.

On the one hand Field Marshal Mohamed Hussein Tantawi did approve last week the appointment of a new ambassador to Israel, but on the other the lower house of the newly elected parliament adopted a declaration stating that Israel was the No. 1 enemy of Egypt and calling for the Israeli ambassador be expelled as well as stopping the sale of natural gas to Israel.

At the same time, it is due to Egypt’s strenuous efforts that the present round of hostilities between Israel and Gaza was brought to an end. Without these efforts it is doubtful that the flare-up could have been halted without an IDF ground operation from Israel which could have ignited the whole region.

The Supreme Council thus demonstrated its pragmatism and the fact that it is well aware of the importance of the relations with Israel – and with the United States. There were many in Israel who were afraid that no new Egyptian envoy would be appointed when the incumbent completed his tour of duty and that relations would be downgraded to the level of a charge d’affaires according to the often repeated wish of the Muslim Brothers and of others who want the peace treaty reopened.

It remains to be seen whether the new ambassador will arrive before the army transfers its powers to a civilian government led by the Brothers.

Regarding the exchanges of fire between Israel and Gaza, the Supreme Council did not want a major problem on its borders at a time when it is desperately trying to deal with a volatile internal situation which could at any minute turn violent.

Equally important, Cairo’s handling of the crisis was a means to show the Arab world that Egypt was still the major player on the Palestinian front.

Not that it was easy, since as usual the Egyptian media lashed at Israel for its alleged atrocities against civilians in Gaza, and even recycled pictures taken during the Cast Lead Operation in January 2009 – but did not mention the hundreds of missiles fired at Israel towns and villages for days on end.

As for the Muslim Brothers, their electoral successes have not been followed by a new awareness of political reality.

The rhetoric of their leaders against Israel has not been dampened, and their tirades have whipped the crowds into a frenzy, leading to the shameful attack on the Israeli Embassy in September and perhaps to the repeated assaults on the pipeline – 13 so far – bringing Egyptian gas to Jordan and to Israel. Stopping the flow has already cost Egypt more than a billion dollars in lost revenues.

The lower house of the Egyptian parliament is powerless to implement its demands regarding the ambassador or the gas, since it has no executive powers; indeed, the government appointed by the Supreme Council in accordance with the temporary constitution does not answer to the parliament and a noconfidence vote would be meaningless. However, it is a clear indication of what the Muslim Brothers have in mind and what they will try to do when they form the next government at some point after a president is elected in June.

Not that the army’s attitude has always been a model of rationality.

It is still hard to understand why security forces let protesters storm the embassy building and reach its doors – in flagrant violation of a number of international conventions.

It is even harder to understand why Tantawi refused to talk with Prime Minister Netanyahu and only a call from President Barack Obama finally spurred him into action.

Perhaps this is due to the generals’ lack of experience: after all, it is not easy to adapt to ruling a huge and heavily populated country when the president has been deposed, civilian institutions are only partially operative and the economy is spiraling down.

This was demonstrated in the way the recent foreign NGO crisis (which has nothing to do with Israel) was handled; having tacitly sanctioned the raids and subsequent legal procedures against these organizations, the Supreme Council then let the American employees leave the country, which led an enraged parliament call for the downfall of the government.

At which point Tantawi made it clear that the government, having been appointed by the Supreme Council, would remain in place until a new president has been elected.

It is to be expected that this dual and ambiguous attitude toward Israel (and the United States) will continue for quite a while. There are some steep hurdles before the end of the transition period. First, a special committee of 100 people must be appointed to draft the new constitution. Then the constitution must be approved by referendum. Only then are presidential elections to be held, it is hoped with the first round taking place on May 23- 24. Should no candidate get 50 percent of the vote, a second round will be held. Final results are expected by mid-June; coincidentally, the verdict in the Mubarak trial is due at the same time.

There is ample room for conflict on any and all those issues, and the people might take to the streets once more. The Brothers with their heavy parliamentary representation will do their utmost to give the constitution a deep Islamic slant while granting more and more power to the parliament at the expense of presidential prerogatives. They will also do their best to ensure that a president with a “true Islamic background” is elected.

The character of the new constitution and president will both have far reaching implications for the nature of relations with Israel. True, Israel and Egypt have common security interests and the dialogue between the relevant services are ongoing, but would a government led by the Brotherhood put a stop to these vital exchanges? What about trade relations, and the sale of natural gas to Israel? What about the existence of Qualified Industrial Zones, which in cooperation with Israel let Egypt export its products – and especially cotton – to the United States without having to pay import duties? Should the agreements be revoked, the entire Egyptian textile industry would be at risk of collapse.

Then there are Sinai, Hamas – which is the Gaza branch of the Muslim Brotherhood, and last but not least, Iran, long seen as an enemy by Hosni Mubarak but which is now trying to ingratiate itself with the new regime.

So many questions... and so few answers.

The writer, a Fellow of The Jerusalem Center for Public Affairs, is a former ambassador to Romania, Egypt and Sweden.

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