By Tom Perry and Yasmine Saleh
CAIRO (Reuters) - Hosni Mubarak's last prime minister, Ahmed Shafik, will soon be free to return from self-imposed exile and perhaps make a political comeback after Egyptian courts on Thursday acquitted him in one corruption case and shelved another.
Shafik left Egypt last year after being defeated in the presidential election by Mohamed Mursi, the Muslim Brotherhood politician since overthrown by the army and now on trial for conspiracy and inciting violence while in office.
U.S. Defense Secretary Chuck Hagel expressed concern about recent charges involving Mursi and other Brotherhood leaders in a phone call with Egyptian army chief Abdel Fattah al-Sisi on Thursday.
Hagel, without entering into specifics at a Pentagon news conference, said he told Sisi such developments alienate some Egyptians, setting back efforts to build a "stable, secure, free democratic Egypt."
Shafik's return would reflect the shift in the balance of power in Egypt since the army removed Mursi and set the Arab world's largest nation on a new course designed to lead to presidential and parliamentary elections next year. The next milestone is a mid-January referendum on a new constitution.
Several corruption cases were brought against Shafik during Mursi's rule, which was cut short by Sisi after mass protests against his rule.
Judicial sources said the court had sent the final case against Shafik back to the prosecutor, who can either dismiss it or order more investigations into the charges, which relate to illegal allocation of state-owned land.
A separate ruling acquitted Shafik and Mubarak's two sons, Alaa and Gamal, in a different corruption case. Alaa and Gamal Mubarak remain in prison on other corruption charges.
The rulings mean Shafik's name will be removed within days from a list of people whose arrest has been ordered, assuming no other cases are filed against him, judicial sources said.
The courts have been a frontline in Egypt's political struggle. Following Mubarak's fall in 2011, an array of cases were brought against the veteran autocrat and his aides.
But the pattern has changed since Mursi's removal: Mubarak has been freed from prison and is now residing at a military hospital, though he is being retried on charges of ordering the killing of protesters in 2011.
This week, the prosecutor unveiled a new case against Mursi and his Brotherhood colleagues, ordering him and 35 others to stand trial for terrorism and conspiring with foreign groups - charges for which they could be executed.
The Brotherhood on Thursday denounced the case, which accuses it of hatching a "terrorist plan" dating back to 2005 and implicates the Palestinian group Hamas, the Shi'ite Islamist government of Iran and its Lebanese ally Hezbollah.
The army-backed authorities have mounted a fierce crackdown on the Brotherhood since Mursi was removed, killing hundreds of his supporters, arresting thousands more and demonizing Egypt's best organized party as a terrorist organization.
"The junta's judges continue to fabricate risible allegations against the democratically elected president and a number of leaders of the Muslim Brotherhood," the Brotherhood said.
The United States, a close ally of Cairo since the 1970s, decided in October to withhold some of its $1.3 billion in annual military aid to Egypt pending progress on democracy and human rights.
Defense Secretary Hagel told Sisi the United States was "committed to the U.S.-Egypt defense relationship", the Pentagon said in a statement after the call.
But he also expressed concern about "recent violence against a non-governmental organization", an apparent reference to a midnight raid on the offices of a civil society group.
A security official said the police had been searching for a democracy activist wanted in connection with protests against a law that heavily restricts the right to demonstrate.
Mohamed Adel, the activist, was arrested, together with five others who were later released.
Secular activists who were critical of Mursi's rule have grown more concerned about the future of political freedoms in Egypt since the army-backed government passed the law, which bans protests without police permission.
The raid targeted an organization run by Khaled Ali, a leftist who ran in last year's presidential election but was knocked out in the first round.
Shafik, a former air force commander who cited Mubarak as a role model during his election campaign, lost narrowly to Mursi in the run-off.
In an interview in September, he said he would not run for the presidency if Sisi did, and that Sisi had his full support.
Sisi has yet to say if he will run. He enjoys wide support among those Egyptians who rejoiced at Mursi's overthrow, but is reviled by the ousted president's supporters. Dates for presidential and parliamentary elections have yet to be set.
(Additional reporting by Maggie Fick in Cairo and Phil Stewart in Washington; Editing by Kevin Liffey)