Raif Badawi was sentenced last year to 10 years in prison, 1,000 lashes and a fine of one million Saudi Arabian riyals (about $315,000 Cdn) for offences including creating an online forum for public debate and insulting Islam.
The flogging will be carried out over a period of 20 weeks, Amnesty International said.
“We received confirmation that the 50 first lashes were given this morning," Mireille Elchacar told the CBC Radio showQuebec AM.
Badawi was first arrested in June 2012 for setting up the "Free Saudi Liberals" website.
Prosecutors had demanded he be tried for apostasy, which carries the death penalty in Saudi Arabia, but a judge dismissed that charge.
Wanted to foster debate
Elchacar said Amnesty International considers Badawi a "prisoner of conscience."
"He just wanted to open debate about the religious subjects, social subjects, political subjects, such topics which are not open to debate in traditional media in Saudi Arabia," Elchacar said.
Amnesty International quoted a witness as saying the flogging took place before the public and security officials in front of the al-Jafali mosque in Jeddah.
"The whole ordeal lasted around 15 minutes. Afterwards, he was put back in the bus and taken away," the group said in a statement.
Amnesty International is calling for Badawi's sentence to be quashed and for him to be released immediately and unconditionally.
On Thursday, the United States asked Riyadh to cancel the sentence of 1,000 lashes.
Wife feared for safety
Badawi's wife and three children settled as refugees in Sherbrooke after his arrest.
EnsafHaider said she feared for the safety of their children and herself in Saudi Arabia. She fled via Egypt, Lebanon, and finally made it to Canada in October 2013.
"I felt threatened by those who demanded Raif’s imprisonment," said Haider.
A protest was scheduled for Friday at 12:30 p.m. ET in Sherbrooke to denounce the sentence.
Badawi's website included articles critical of senior Saudi religious figures and others from Muslim history.
Saudi Arabia's legal code follows sharia Islamic law. Judges are trained as religious scholars and have broad scope to base verdicts and sentences on their own interpretation of religious texts.
Saudi Arabia on Wednesday condemned the killings of 12 people in an attack on a French satirical newspaper which had lampooned Islam. But it has also in the past called for an international law to criminalize insults to the world's main religions.