An Egyptian court released a detailed ruling on Sunday on why it sentenced three journalists working for al-Jazeera English to three years in prison for airing what it described as “false news” and biased coverage. The case has long been criticised by press freedom campaigners and others.

The ruling, published by the state news agency Mena, said Mohamed Fahmy, a Canadian national, Peter Greste, an Australian journalist, and BaherMohamed, an Egyptian producer, were by default members of the banned Muslim Brotherhood group, which Egyptian authorities consider a terrorist organisation.

“It has been proven beyond reasonable doubt that the al-Jazeera media channel has dedicated its broadcasting to the service and support of the Muslim Brotherhood faction and that they have permanently sided with them at the expense of their media ethics,” the ruling said. “This provides enough ground for a conviction of belonging to a group based on violations of the law.”

The ruling also said the three operated without press credentials and secretly worked at the Marriott hotel in central Cairo without a permit. The journalists and the network deny the accusations. Al-Jazeera said it would appeal.

After last weekend’s ruling, Mohamed and Fahmy were imprisoned, while Greste had been deported previously.

The case, which was widely condemned by the international community, has become an embarrassment for the Egyptian president Abdel Fatah al-Sisi.

Last week, the human rights lawyer Amal Clooney, who acts for Fahmy, said Sisi must pardon the men.

“It’s ironic that the conviction was for tarnishing Egypt’s reputation when ... this [case] is what’s tarnished Egypt’s image,” Clooney told the BBC. “I do think he’s aware of that and he has a way to fix it.”

The long-running trial is entangled in the wider political conflict between Egypt and Qatar, where al-Jazeera is based, following the Egyptian army’s 2013 military ouster of the Islamist president, Mohamed Morsi, a Brotherhood member.

Evidence presented at the trial ventured into the absurd, including music videos and footage of animals, which defence lawyers and even the judge dismissed as irrelevant. Third-party observers said no evidence proved the charges. Critics describe the case as politically motivated.

The men are seeking a pardon from Sisi, who personally expressed regret over the trial and the damage it had done to Egypt’s reputation. He has said it would have been better to simply deport the journalists.

Al-Jazeera had been waiting for Sunday’s detailed ruling, which could have been released up to 30 days after the verdict, to appeal.

The case began in December 2013, when Egyptian security forces raided the hotel suite used by al-Jazeera at the time to report from Egypt.

The journalists began using the hotel as a base of operations after the al-Jazeera English office near Tahrir Square was raided by police. Authorities arrested Fahmy, Greste and Mohamed, later charging them with allegedly being part of the Muslim Brotherhood, and airing falsified footage intended to damage national security.

The three men initially were convicted on 23 June 2014, with Greste and Fahmy sentenced to seven years in prison and Mohamed to 10 years for also being found with a spent bullet casing. That ruling was later overturned on appeal by Egypt’s court of cassation, the final stage of criminal appeals, which said the initial proceedings were marred by violations of the defendants’ rights. However, a retrial was ordered, ending with last week’s convictions.

The detailed ruling in the initial 2014 conviction said that the journalists had been brought together “by the devil” to destabilise Egypt. The detailed ruling released on Sunday made no such reference.