CAIRO // The presidential pardon of 26 Islamists from Egyptian prisons revealed for the first time the contours of Mohammed Morsi's powers.
The security services, or mukhabarat, only permitted the release half of the 52 men that Mr Morsi had submitted on a list for approval, highlighting the fraught relations between the president and the same spies and security officials who once tracked groups such as the Muslim Brotherhood.
Mr Morsi was a long-time member of the Brotherhood, an Islamist group whose members were regularly arrested and sentenced to prison on trumped-up charges by Hosni Mubarak's regime. Mr Morsi formally withdrew from the group before his inauguration.
Yet, Mr Morsi's pardon suggested his sympathies still lie with members of the group and other Islamist organisations, such as Gama'a Islamiya and Al Jihad.
So it was no surprise that he sought the release of Islamist inmates as part of a Ramadan amnesty from the presidency. He had spent several years in prison on charges of belonging to a banned group that the Mubarak regime saw as its greatest threat.
An official notice in the governmental gazette listed the names of the 26 to be pardoned, none of whom were high-ranking members of the Islamist groups, although some faced the death penalty. Sixteen were from Gama'a Islamiyya and Al Jihad, and eight were from the Brotherhood, according to the gazette.
The rest were denied their pardons on grounds of national security, according to Tariq El Zomor, who is the a leading member of the political arm of the Gama'a Islamiyya, the Building and Developmenty Party. Mr El Zomor served 30 years in prison - along with his cousin Abboud - for their role in the assassination of President Anwar Sadat in 1981 before being released last year.
"The president does not have full control of these things," Mr El Zomor said. "Not all of his requests for release were met by the security services."
Even before Mr Morsi was inaugurated on June 30, a power struggle was imminent. The Supreme Constitutional Court of Egypt ruled before the elections that part of parliamentary elections had been unconstitutional and called for parliament to be disbanded.
The Supreme Council of the Armed Forces (Scaf) dissolved parliament, but it also enacted a new constitutional declaration that stripped the presidency of some of its roles and made Scaf the de facto legislator in place of the old parliament. Islamist groups, such as Mr Morsi's Freedom and Justice party, had controlled more than 70 per cent of the parliament.
The presidency and the military are still waging a proxy battle through the courts over their powers and the rewriting of the constitution.
The refusal of some of the pardons by the mukhabarat reveals another front on which Mr Morsi faces opposition from a state institution.
Agencies such as the State Security and Egyptian General Intelligence Services (EGIS) were the primary tools of repression of Islamist groups under Mubarak.
The head of the EGIS was Omar Suleiman, who died this month of health complications in the United States. Suleiman waged a relentless and often brutal war on extremists and struck a deal for the US to send suspects of terrorism to Egypt through "extraordinary renditions" for further interrogation and in many cases, torture.
The January 25th uprising that forced Mubarak to step down heralded a new era for followers of political Islam who had been jailed by the old regime. The army allowed hundreds of inmates who had fulfilled or served at least half of their sentence to go free.
In March, several of the most prominent Islamist prisoners were released after winning a court appeal. The eight men included Mohammed Al Zawahiri, the brother of Al Qaeda chief Ayman; Mohamed Shawki Islamboli, whose brother Khaled, an Egyptian military officer, was convicted of the assassination of Sadat and executed by a firing squad; and Said Imam Fadl, a religious leader and author of texts used by militants in Afghanistan.
Only a few dozen Islamists still remain in prison and they are attempting to win the same release that Mr Al Zawahiri won through a separate court appeal. They were, however, marked as security risks by the security forces and not granted release, despite Mr Morsi's request for their pardons, according to Mr El Zomor.
These include Rifai Taha, a former emir of Gam'a Islamiyya, and Mostafa Hamza, the alleged mastermind of the assassination attempt on Hosni Mubarak in Ethiopia in 1995 and a Gama'a Islamiyya member.
Ali Soufan, a former special agent for the US Federal Bureau of Investigation (FBI), said he believed it was reasonable to release Islamists from prison as part of a new era of religious and political freedoms.
But he questioned the president's focus on high-profile Egyptians who have been convicted of acts of terrorism, such as Omar Abdel-Rahman, better known as the Blind Sheikh who was given a life sentence by a US court for his role in the 1993 bombing of the World Trade Centre in New York. Mr Morsi had said in a speech in Tahrir Square before his official inauguration that he would press the US to release Abdel-Rahman.
"I'm not one of those guys who is against an Islamist coming to power in Egypt," he said. "But some of these decisions and announcements make me wonder who is he trying to cater to? 99 per cent of Egyptians don't care about Abdel-Rahman. Why is he focusing on him?"
Mr Soufan played a lead role in investigations into some of the most prominent cases involving Islamist extremists in the 1990s and early 2000s.