Mohammed Morsi's comments came during a visit to the northern Sinai city of el-Arish, where he prayed at its main mosque and met with tribal leaders and top ultraconservative Salafi clerics. He also met with Christian families who were lately forced to leave their homes in the area after getting death threats from Islamic militants.
Troops were on high alert, deployed at entrances and exits of the city as Morsi gave a speech, assuring tribal elders that "sons of Sinai" will not be pursued and that that the judiciary would review many of the cases from the region.
"The era of blackmailing, abuse and discrimination among Egyptians is over and will not come back," he said.
Extremist militants operate in disparate groups in Sinai and are believed to have grown in numbers since last year's political upheaval following the ouster of autocratic President Hosni Mubarak, Morsi's predecessor.
The surge in militancy has largely been due to a security vacuum in the aftermath of the popular uprising that toppled Mubarak and heavy weapons smuggled from Libya across the desert to Sinai, which links Egypt's borders with the Gaza Strip and Israel.
In a brazen attack, unidentified militants killed 16 Egyptian soldiers near the border in August and last month, heavily armed militants wearing explosive belts opened fire on Israeli soldiers near the border, killing one.
Under Mubarak, Sinai's largely nomadic Bedouin population was long neglected and discriminated against. As a result, the region became a hub of weapons, drugs and human trafficking. Cities and towns bordering Israel and Gaza live off smuggling across borders and underground tunnels.
Mubarak's regime often rounded up hundreds of Sinai young men, held them without charges or sentenced them before military tribunals, delivering swift and harsh verdicts.
Morsi, who hails from the fundamentalist Muslim Brotherhood whose members have been routinely rounded up and tried under Mubarak, has sought to reverse the perception of security sweeps, police torture and abuse by the authorities—even as he launched military operations to hunt down perpetrators of the August attack.
"A decision has been taken to review cases of those (from Sinai) who were tried in absentia," he said during Friday's visit.
He also hinted that death penalties against 14 members of an extremists group from Sinai may be waived or reduced.
"I have not signed a single death sentence since I assumed power," Morsi said.
The 14 were convicted for a June 2011 attack against el-Arish's main police station and a nearby bank that killed a civilian and a number of police and military officers. The group was also found guilty of storming el-Arish's police station and of smashing statues of former President Anwar Sadat who was assassinated in 1981 after signing Egypt's peace treaty with Israel.
Since his election in late June, Morsi has ordered the release of dozens of top Islamic militant leaders sentenced to life imprisonment or given death sentences on terrorism-related charges, including those convicted of assassination attempts against Mubarak.
Some Sinai clerics who met with Morsi on Friday were skeptical of his promises.
"The president has made many promises now and before as well, but so far we have seen nothing," said Abu Faisal, one of the region's leading Islamists.