An Egyptian court has sentenced Canadian Mohamed Fahmy and two other Al-Jazeera English journalists to three years in prison, the latest twist in a long-running trial criticized worldwide by press freedom and human rights activists.

Fahmy faced widely denounced terror charges and had spent more than a year in prison before a successful appeal of an earlier conviction resulted in the re-trial that culminated in Saturday's verdict.

In his ruling, Judge Hassan Farid said he sentenced the men to prison because they had not registered with the country's journalist syndicate. He also said the men brought in equipment without the approval of security officials, had broadcast "false news" on Al-Jazeera and used a hotel as a broadcasting point without permission.

It wasn't immediately clear how the sentence would affect the three men, but they are seeking a pardon from President Abdel-Fattah el-Sissi, who has personally spoken out against the case. Al-Jazeera said it will also appeal the verdict, once the court releases its full ruling in the next 30 days.

Immediately after the ruling, Fahmy's wife, Marwa, wept in the court.

Speaking to CBC News, she called on Prime Minister Stephen Harper to step in and save the Canadian, who gave up his Egyptian citizenship earlier this year.

"What I'm asking for right now is Mr. Harper to interfere," she said. "It's time for him to prove that he can help and support a Canadian citizen" that he knows is innocent.

"I believe this [verdict] is extreme injustice and extremely unfair," she said.

Mohamed Fahmy's colleague reacts to prison sentence5:47

Hoping for deportation

Marwa and Fahmy's brother, Adel, said they are hoping Fahmy will get the same treatment as Peter Greste, one of the Al-Jazeera journalists who was charged Saturday but deported to his native Australia in February.

"We're done in relying on or putting any hope on the judicial process, because it is very obvious that it is meaningless," Adel Fahmy told CBC News.  

CBC's Derek Stoffel was in the courtroom and spoke to Canada's ambassador to Egypt Troy Lulashnyk immediately after the verdict.

APTOPIX Mideast Egypt

Marwa Fahmy, wife of Canadian Al-Jazeera English journalist Mohamed Fahmy, bursts into tears as she is watched by human rights lawyer Amal Clooney after hearing the verdict. (Amr Nabil/Associated Press)

"Obviously Canada is deeply disappointed in the outcome of this process," Lulashnyk said. "Canada has consistently called for Mr. Fahmy's full and immediate release. And this is what we will continue to be doing. While he is in Egypt we will continue to provide him the consular support necessary and will be following up with officials."

Lynne Yelich, the minister of state (Foreign Affairs and Consular), released a statement early Saturday saying the decision "undermines confidence in the rule of law in Egypt," and called for Fahmy's "immediate return" to Canada.

Outside the court Fahmy's high-profile human rights lawyer, Amal Clooney, told reporters the verdict had sent an ominous message.

"It sends a message that journalists can be locked up for simply doing their job, for telling the truth and reporting the news. And it sends a dangerous message that there are judges in Egypt who will allow their courts to become instruments of political repression and propaganda," she said.

Clooney added that she hoped el-Sissi would pardon the three journalists.

'Defies logic and common sense'

Al-Jazeera English acting director-general said the verdict "defies logic and common sense."

"The whole case has been heavily politicized and has not been conducted in a free and fair manner," Mostefa Souag said.

"There is no evidence proving that our colleagues in any way fabricated news or aided and abetted terrorist organizations and at no point during the long drawn out retrial did any of the unfounded allegations stand up to scrutiny."

The 41-year-old Fahmy's troubles began in December 2013 when he was working as the Cairo bureau chief for Qatar-based satellite news broadcaster Al-Jazeera English.

Mohamed Fahmy

Canadian journalist Mohamed Fahmy (centre), his wife Marwa, left and human rights lawyer Amal Clooney, right, await the verdict earlier Saturday. (Derek Stoffel/CBC)

He, Greste and Egyptian producer Baher Mohammed were abruptly arrested and charged with a slew of offences, including supporting the Islamist Muslim Brotherhood, a banned organization affiliated with ousted Egyptian president Mohammed Morsi, and with fabricating footage to undermine the country's national security.

The trio maintained their innocence throughout, saying they were just doing their jobs, but after a trial which was internationally decried as a sham, they were found guilty and sentenced to prison terms.

Greste was suddenly allowed to leave Egypt before their retrial began, under a law which allows for the deportation of foreign nationals convicted of crimes.

Greste told CBC News he wants more than deportations; he wants all three of them pardoned, noting that even though he's in Australia he's technically a convicted terrorist and can no longer travel to countries that have an extradition treaty with Egypt.

"This has to do with fundamental principles of freedom of speech, of rule of law, of due process — and the Egyptian president now has the ability to correct this injustice," he said. 

Gave up dual Egyptian citizenship

Fahmy gave up his dual Egyptian citizenship while behind bars in the hopes that he could follow the same path as Greste, but that didn't happen. He was, however, granted bail in February shortly after his second trial got underway.

Throughout the proceedings, Fahmy has pointed out that his case had been complicated by politics in the Middle East, referring to himself as a "pawn" in a rift between Egypt and Qatar, which owns Al-Jazeera.

Amnesty International noted in a statement that the court also sentenced a larger group of Egyptians on similar charges to three years, including students who said that security forces had beaten them following their arrest last year. 

"The authorities should ensure a prompt, independent and impartial investigation is conducted into the defendants' allegations of torture and other ill treatment," the statement said.

Mohamed Fahmy's brother reacts to verdict1:23

With files from CBC News and The Associated Press