By Tom Perry and Omar Fahmy
CAIRO (Reuters) - Egypt's deposed Islamist president, Mohamed Mursi, and 129 others including members of Hamas and Hezbollah, were referred to trial on Saturday on murder and other charges related to a mass jail break during the 2011 uprising against Hosni Mubarak.
These are the third set of charges brought against Mursi since he was ousted by the army in July amid street protests against his rule and they intensify the relentless repression of his Muslim Brotherhood group in the months that followed.
Earlier this week, the prosecutor ordered Mursi and 35 other Brotherhood leaders to stand trial in a separate case that charges them with plotting with foreigners including Hamas and Hezbollah to carry out a terrorist conspiracy against Egypt.
Those charges, described as "risible" by the Brotherhood, could result in the death penalty for Mursi and his colleagues.
On Thursday, U.S. Defense Secretary Chuck Hagel expressed concern about the charges against Mursi and other Brotherhood leaders in a phone call with army chief General Abdel Fattah al-Sisi, the man who ousted Egypt's first freely elected leader.
Sisi is widely seen as the person most likely to win a presidential election expected next year were he to run. The next stage in the army's transition plan is a mid-January referendum on a new constitution.
The security forces have killed hundreds of Brotherhood supporters in the streets and arrested thousands more. The government accuses the group, previously Egypt's best-organized political and religious movement, of turning to violence and terrorism - charges the Brotherhood denies.
In a three-page statement, investigating judge Hassan al-Samir described the new case, relating to prison breaks during the anti-Mubarak revolt, as "the most dangerous crime of terrorism the country had witnessed".
Samir said he had uncovered a "terrorist plan" hatched by the Brotherhood long ago and carried out with foreign players including Lebanon's Shi'ite militant Hezbollah movement and the Palestinian Islamist Hamas group which rules the Gaza Strip.
Mursi was one of those who escaped from prison after being rounded up with other Brotherhood leaders after the 18-day uprising that toppled Mubarak broke out on January 25, 2011.
In a telephone interview with Al Jazeera immediately after he left prison, Mursi said the jail had been opened by locals with no instructions from Brotherhood leaders. He said he and other Brotherhood leaders had not fled and were looking for representatives of the prosecution to report what had happened.
Samir's statement did not name the accused Hezbollah or Hamas members. A judicial source said 68 of them belonged to Hamas. At least one Hezbollah operative jailed in Egypt escaped during the chaos in 2011. He then fled to Lebanon.
An ideological cousin of the Muslim Brotherhood, Hamas had been part of an alliance including Hezbollah until the Arab Spring uprising redrew the political map of the region. Mursi's opponents demonized the Palestinian group during his year in office, accusing it of scheming against Egypt.
Mursi and his comrades, including Brotherhood leader Mohamed Badie, were charged with killing and kidnapping policemen, attacking police facilities and carrying out the prison break.
After protests against Mubarak began, the prosecutor said, the Brotherhood, extremist groups and more than 800 militants who had infiltrated from Gaza staged attacks on police before assaulting three prisons to release their allies.
At least 50 police and prisoners were killed in the raids in which at least 20,000 criminals escaped, Samir's statement said.
The accused were also charged with kidnapping four policemen and holding them in the Gaza Strip. It also said the men had "appropriated animal and poultry livestock" from the prisons.
The judicial source said Sheikh Yusuf al-Qaradawi, a prominent cleric based in Qatar, was among the accused.
The charges brought against Mursi and the Brotherhood this week formally implicate them in violence against security forces in the Sinai Peninsula, the desert territory bordering Israel where militant attacks spiked after Mursi's overthrow.
Some 200 soldiers and policemen have been killed since then.
The cases also bring formal charges against members of Mursi's presidential staff who had been held without charge since July. These include Essam El-Haddad, his national security adviser, who is accused of divulging state secrets to Hezbollah, Hamas and the Iran's Revolutionary Guards.
Haddad and another presidential aide, Ayman Ali, were both transferred to a maximum security prison on the outskirts of Cairo on Saturday, a security official said.
The army-backed authorities have in recent weeks also charged secular activists in connection with protests organized in defiance of a new law that restricts the right to assembly.
In a move criticized by activists as an escalation against dissenters, the police raided the offices of a prominent rights organization this week, holding five activists for nine hours and arresting another sought in connection with protests.
New York-based Human Rights Watch said on Saturday that the Egyptian security forces had "expanded their harassment of political activists", saying the government was targeting voices demanding "justice and security agency reform".
(Writing by Tom Perry; Editing by Alistair Lyon and Alison Williams)