"We will control all parts of Sinai,” Egyptian President Mohammed Morsi vowed in an off-the-cuff speech he gave after Sunday’s terror attack in which 16 Egyptian soldiers were killed at a military base in Sinai. However, the question of how to implement such “control” reveals a disagreement between Morsi and his defense minister, Gen. Hussein Tantawi.

While the president believes that Hamas can exert its influence on at least some of the terror organizations operating in Sinai through putting pressure on their “clients” in Gaza, Tantawi sees Hamas as part of the problem and is far from accepting it as an effective partner in the Sinai conflict.

Egyptian sources said that Tantawi “twisted Morsi’s arm in the decision to close the Rafah Crossing indefinitely” – and this comes only two weeks after Morsi decided to extend the crossing’s opening hours and facilitate easier movement from both directions.

Steps taken by Hamas leader Khaled Meshal, such as erecting a mourners’ tent in Gaza and sending condolences to Morsi on the death of the soldiers – have not convinced Tantawi. Contrary to the Israeli stance, he is skeptical of Hamas’ ability to control all of the organizations operating in Gaza and still believes, as he always did, that Hamas’ slackness has contributed directly to the establishment of armed separatist organizations with which Hamas is forced to maintain a conciliatory relationship.

It is interesting to note that Sheikh Nabil Naim, one of the leaders of Egypt’s extreme Islamic movement called the Jihad Group, supports the military’s stance. In an interview to Saudi newspaper Asharq al-Awsat, he said that Hamas currently prefers to refrain from attacking Israel so as not to risk an Israeli attack on Gaza, and therefore concludes that Hamas would rather have other organizations to do its work.

On the other hand, the Muslim Brotherhood claims it was the policy of former president Hosni Mubarak – together with Tantawi – that led to the deep neglect of the Bedouin in Sinai and thus gave rise to burgeoning terrorist enclaves. Sources in Egypt say Morsi wants to differentiate himself from the former regime, but now finds himself in an impossible position.

Moreover, as Morsi confronted the military’s policies and pressure, he also faced a call on Tuesday by Muslim Brotherhood Supreme Guide Mohammed Badie to amend the Camp David accords and allow the military to deploy its forces in sensitive areas, allowing Egypt to control the entire Sinai Peninsula. So far, Morsi has been less than willing to coordinate politically with Israel (besides the coordination on security matters), which is why he passed on appointing a foreign minister from his own party.

The Egyptian military does not have any magical solutions, either. One of the main problems is mapping out the organizations operating in Sinai. The tendency to categorize all of them as "global jihad" groups or Al-Qaida-affiliated organizations – meaningless terms that do not help in sorting them out according to their objectives and capabilities – only complicates the struggle against them.

The Al-Takfir organization, for example, is different from the Al-Hijra movement, and both often do not cooperate with other jihadist organizations. Some of the organizations recruit volunteers from the Palestinian territories, Kuwait, Yemen and other countries, while others maintain solely Egyptian operatives. Some movements seek to harm the Egyptian government, while others see the struggle against Israel as their raison d'être. This mixture of organizations is also exploited by the Bedouin – some seek income from arms smuggling while others join the ranks for ideological reasons.

The Hamas leadership is trying to convince Morsi that it is capable of cooperation, at least on the intelligence level, and Hamas leaders – namely Ismail Haniyeh and Khaled Meshal – went as far as offering concrete assistance to Morsi and the Muslim Brotherhood leadership. However, Tantawi has so far showed little enthusiasm for the proposals of Hamas – a movement that up until a few months ago was still financially supported by Iran.

The strategic differences between Morsi and Tantawi over Hamas’ role may have repercussions on the conflict in Sinai – and on Egyptian politics. The criticism hurled at Morsi by both secular and religious adversaries, the upcoming crucial parliamentary election and the realization that the Muslim Brotherhood has the same tools that Mubarak had with which to confront the security situation in Sinai, may take a toll on the Brotherhood in these elections.

Morsi will therefore have to show more determination than the military on security matters and try to overshadow his defense minister – who is, in fact, his security boss – Gen. Tantawi.

Read this article in Hebrew