Egyptian experts warned human rights barrister Amal Clooney that she risked arrest in February 2014 after identifying serious flaws in its judicial system.

The same flaws subsequently contributed to the conviction of three al-Jazeera journalists now jailed in Cairo.

In an interview with the Guardian after their appeal hearing this week, Clooney, a lawyer for one of the trio, said they were victims of the same legal irregularities that she earmarked in her February 2014 report about Egyptian courts.

Written before Clooney became involved in the al-Jazeera case, the report was deemed so controversial that her team was warned they could be arrested should they have tried to present its findings inside Egypt.

“When I went to launch the report, first of all they stopped us from doing it in Cairo,” Clooney told the Guardian. “They said: ‘Does the report criticise the army, the judiciary, or the government?’ We said: ‘Well, yes.’ They said: ‘Well then, you’re risking arrest.’”

The report, compiled on behalf of the International Bar Association, said Egypt’s judicial system was not as independent as it could be. It pointed out that officials in the ministry of justice have wide powers over nominally independent judges, and highlighted the control the government can exert over state prosecutors.

Among other recommendations, Clooney and her co-authors suggested ending the practice that allows Egyptian officials to handpick judges for certain politicised cases. “That recommendation wasn’t followed, and we’ve seen the results of that in this particular case where you had a handpicked panel led by a judge who is known for dispensing brutal verdicts,” Clooney. said “And this one was no different.”

The three journalists – Peter Greste, Baher Mohamed, and Mohamed Fahmy, whom Clooney represents – were initially sentenced to between seven and 10 years in jail last June by the controversial Egyptian judge Mohamed Nagy Shehata.

Baher Mohamed, Mohamed Fahmy and Peter Greste in court in Cairo in March. Photograph: Heba Elkholy/AP

Shehata became notorious during the trial for rarely taking off his aviator sunglasses, mocking Fahmy’s fiancee, and for cracking a joke about World Press Freedom day. A few months later, he also sentenced to death 188 people, Clooney said, “in one mass trial which didn’t distinguish between each defendant’s criminal responsibility”. Shehata failed to respond to several requests for interview.

At the trio’s appeal on New Year’s Day, a new judge refused to throw out the case, but agreed to a retrial, after recognising problems with the initial process. But Clooney fears those flaws – which included the presentation of a Gotye song, footage of a trotting horse, and pictures of Greste’s parents as evidence of the trio’s guilt – are so serious that they will compromise the integrity of any second hearing.

“If the idea is: well, there were errors and now there’s going to be a retrial, but then the retrial operates on the same basis as the original one, that doesn’t really mean much,” Clooney said. She has waived most of her usual fees, and is paid directly by Fahmy without the support of al-Jazeera. “I don’t see how the prosecution can proceed again in a trial process even if the judges were to be constituted properly this time around. I don’t see how they could fix the lack of evidence.”

As a result, Clooney has concluded “that we have to continue and double our efforts to achieve his release in other ways. Unfortunately we have to conclude that we can’t rely on these Egyptian court processes to achieve a fair or swift result.”

For Baher Mohamed, the third detainee who holds only an Egyptian passport, his fate largely depends on those court processes, with the prospect of a presidential pardon dwindling. But Clooney’s client, Fahmy, a Canadian citizen, and his Australian colleague Greste, have another option: deportation to their home countries.

Fahmy and Greste have applied to Egypt’s chief prosecutor to demand they be sent to Canada and Australia respectively under the terms of a new presidential decree that provides foreign detainees with such a route, and which seems to have been tailored for their case.

The vague and unprecedented nature of the decree has led to doubts about how it would be used in practice. But based on her communication with relevant officials in Egypt and Canada, and on her experience of international law, Clooney is hopeful that deportation is a real option. “There are many different ways in which the transfer from Egypt to Canada can occur, and as long as there is a genuine commitment on both sides, I see no reason why a transfer can’t happen in fairly quick terms.”

Inside Egypt, Fahmy’s appeals team was led by an Egyptian lawyer, Negad Boraie, with contributions from Clooney that related to international law. But outside Egypt, it is Clooney who is spearheading attempts to secure Fahmy’s deportation, and hopes next week to meet the Canadian foreign minister, John Baird, to try to convince him to expedite the process.

“We are very much hoping that the Canadian and Egyptian officials we have contacted will engage with us fully to ensure that Mohamed is involved – through his counsel – in the discussions and that a fair outcome can be achieved as soon as possible.”

Responding to the allegation that Clooney was told she risked arrest in 2014 if she presented her report in Egypt, a spokesman for Egypt’s police, Hany Abdellatif, later said that she was not listed for arrest.

“There is nothing against Mrs Amal,” Police general Hany Abdellatif told the Guardian. “Maybe someone deceived her. Maybe members of the Muslim Brotherhood [an Egyptian opposition group] or others to delude her that there are no freedoms in Egypt.”

• This article was amended on 2 January and 5 January 2015. Due to editing errors, the headline and text in an earlier version gave the impression that Amal Clooney risked arrest in connection with her representation of one of the al-Jazeera journalists. In fact she was warned in February 2014, before her involvement in the case, that she risked arrest as a result of a report in which she earmarked flaws in the country’s judicial system. This has been corrected. The article and headlines were further amended on 6 January 2015 to make clear that Clooney was warned by experts in Egyptian affairs. An earlier version said she was warned by officials. The article was also amended on 4 January 2015 to include comments from the Egyptian police.