The National Council of Canadian Muslims and two civil liberty organizations say they are "deeply troubled" by recent allegations of religious and racial discrimination within CSIS, and are demanding the federal government take "urgent, proactive and genuine" action to protect the rights of visible minority spies in the workplace.

"Public confidence in the agency demands public accountability," says a letter that was hand-delivered to Public Safety Minister Bill Blair in Ottawa earlier this week. "A categorical culture shift inside CSIS must be demonstrated before the public's trust can be regained."

The letter is in response to CBC News stories last week about a lawsuit from a longtime analyst in Canada's intelligence service who alleges his Muslim faith marked him as a target for harassment, emotional abuse and even physical assaults.

His statement of claim, filed under an identity-masking pseudonym in Federal Court earlier this month, outlines what it says was a pattern of bullying and prejudice stretching back almost two decades that saw the man treated as a "second-class citizen" by co-workers and management.

Among its most disturbing details is an allegation that the agent was humiliated and assaulted while he prayed in his office by colleagues who would utter profanities and throw open his office door, hitting him in the head or body, as he kneeled on the carpet.

"I don't think there is anybody in terms of the class of employees lower than the practising Muslim at the service," the analyst told CBC in an exclusive interview.

Letter questions CSIS's 'organizational culture'

The letter to the public safety minister, also signed by the Canadian Civil Liberties Association and the International Civil Liberties Monitoring Group, references past lawsuits by minority CSIS employees that were eventually settled out of court. It also questions the spy agency's repeated claims that it has zero tolerance for discrimination in its workplace.

"The fact that Muslim and other minority CSIS employees have resorted to suing the agency in order to come forward and be heard raises many questions about the agency's organizational culture, and its commitment to resolving its issue beyond making vague public statements," the letter reads.

It also expresses concern that the agency's culture of "total secrecy" might be inhibiting other affected employees from bringing misconduct complaints forward, or enabling managers to punish those who dare to voice objections about mistreatment.

"Retaliation by such agencies against truth-tellers is easy and devastatingly effective," it warns.

A longtime employee is suing Canada's spy agency for racial and religious discrimination. In this exclusive interview, the man — who can't be identified by law — tells CBC News how his co-workers allegedly reacted when he would pray in his office. 1:37

As such, the three groups are asking Ottawa to extend federal whistleblower protections to CSIS employees, or give intelligence oversight bodies the explicit power to look into workplace complaints.

"We're not advocating that these agents or employees reveal any sort of state secrets that would put security at risk," said Sameha Omer, director of legal affairs for the National Council of Canadian Muslims. "What we're advocating for is that agents be able to be protected under whistleblower legislation. For them to be able to come forward internally, to be able to make that complaint, they need to know that even if they do come forward, they're not going to face any sort of reprisal."

Looking for more disclosure

The NCCM and the other signatories would also like more disclosure about the spy agency's efforts to recruit and promote minorities within its ranks, suggesting that the government mandate "Diversity, Equity and Inclusion" audits at least once every five years and share the results with the public.

A 2014 equity audit, released under Access to Information legislation, showed that 14.4 per cent of the spy agency's 3,000 employees were visible minorities, while 3.6 per cent had disabilities and two per cent were Indigenous. At the time, none of CSIS's senior managers were minority or Indigenous, and only 17 per cent were female.

If this is how they treat a colleague ... particularly someone of the Muslim faith, then what does that signal to the communities that they are meant to be protecting? - Tim McSorley, national co-ordinator, International Civil Liberties Monitoring Group

Tim McSorley, the national co-ordinator of the International Civil Liberties Monitoring Group — a coalition of 45 NGOs, unions, professional associations, faith groups and environmental organizations — said the allegations of discrimination within CSIS raise questions about the agency's external mindset, too.

"It really resonates around those issues of how CSIS approaches the Muslim community at large, if this is what happens to people within their own workplace," McSorley said. "If this is how they treat a colleague and how they react to somebody's background and religion in the workplace, particularly someone of the Muslim faith, then what does that signal to the communities that they are meant to be protecting?"

McSorley said his group is hopeful that the Liberal government will take meaningful action to make the intelligence service more accountable to both Parliament and the public.

"[The government] has talked a lot about bringing more transparency," he said. "I think this provides another real opportunity to them to make good on that."

A close-up view of a portion of a discrimination lawsuit filed against Canada's spy agency in federal court last week. (John Lesavage/CBC)

Blair's office declined an interview request, but a statement provided to the CBC says that he is concerned about all allegations of harassment and discrimination.

"We are committed to ensuring that our security agencies are worthy of the trust of Canadians and we are committed to strengthening accountability. Across all agencies and departments, our government will strive to ensure that all employees are treated with fairness, respect and dignity, and we will work tirelessly to foster a workplace that is safe for all," it reads.

But Omer said that platitudes about diversity and inclusion won't suffice this time, and that the National Council of Canadian Muslims needs to know what steps CSIS has already taken to confront discrimination in the workplace — and what more they will do in the face of the new allegations.

"Our organization, our community itself, they want answers," she said. "We do want to know what happened."