An Egyptian criminal court has acquitted an Irish-Egyptian man kept in pre-trial detention for four years who says he was regularly tortured during his incarceration.

Ibrahim Halawa - arrested at age 17 as part of a deadly crackdown on protests in Cairo and who faced the death penalty - has yet to walk free following Monday's verdict, said defence lawyer Yasmeen Said.

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Hawala and his three sisters were arrested along with hundreds of others in August 2013, days after security forces violently broke up a sit-in by supporters of then-president Mohammed Morsi, who had been overthrown by the military the previous month.

The sisters were released three months later on bail, but Halawa was kept in custody.

UK-based international human rights organisation, Reprieve, which is assisting Ibrahim, said in a statement Monday's verdict was "long overdue".

"Ibrahim was arrested as a child for the 'crime' of attending a protest, tortured, and tried facing the death penalty alongside adults in an unfair mass trial," said Maya Foa, director of Reprieve.

"For years, these court proceedings - which were designed to punish political dissent - made a mockery of justice."

She also said the Irish government and others "must now not rest until Ibrahim is at home in Ireland".

"The wider international community - including the EU, which helps to fund Egypt's courts - must also call urgently on Egypt to end its use of patently illegal mass trials," she said.

Irish Prime Minister Leo Varadkar welcomed Halawa's acquittal and said the case had been an "extraordinarily protracted" one.

"Now that Ibrahim has been cleared of all charges, I expect he will be released as soon as possible and can return home to his family. The government will facilitate his return home at the earliest opportunity," Varadkar said in a statement.

'Prisoner of conscience'

The court on Monday sentenced 43 defendants to life imprisonment (25 years under Egyptian law), 399 defendants were sentenced to between five and 15 years, and 52 were acquitted, including Halawa.

Najia Bounaim, North Africa research director at Amnesty International, said Ibrahim was "a prisoner of conscience who should never have been detained in the first place".

"Ibrahim Halawa's acquittal puts an end to the gross injustice in his case. However, it is utterly disgraceful that at the same time the Egyptian authorities have handed out heavy sentences to 442 others after sham proceedings in a mass trial that flouted the most basic standards of a fair trial, while security forces who used excessive and lethal force during protests that day have escaped unpunished," she said.

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Halawa was arrested on August 16, 2013 - a day of violence centred around a mosque in Cairo's central Ramses Square. Dozens were killed and scores wounded in clashes between Morsi supporters and police.

Halawa's health has deteriorated over the years, with the young man protesting his detention with several hunger strikes. He has lost at least 30kg, according to his family.

US-based Human Rights Watch says the Egyptian government has arrested, charged, indicted or sentenced tens of thousands of people during unfair trials.