That's largely because they've been subject to new, high-stakes tax audits into their political activities that could strip them of their coveted charitable status.
But perhaps for the first time, some of their voices are being heard unfiltered.
Gareth Kirkby, a former journalist and now graduate student in communications, interviewed the leaders of 16 such groups for a master's thesis at Victoria's Royal Roads University, offering them anonymity in return for candid assessments of their predicaments.
Kirkby found evidence for what he called "advocacy chill" among charities who've been subject to some of the dozens of political-activity audits being conducted by the Canada Revenue Agency.
"The data suggest that the current federal government is corrupting Canada's democratic processes by treating as political enemies those civil-society organizations whose contributions to public policy conversations differ from government priorities," concludes Kirkby's MA thesis, accepted last month by the university after vetting by academic supervisors.
"What is unprecedented is the ... coupling of that rhetoric with action. This action entails specifically politicized use of the associated governmental regulatory body (the Charities Directorate at CRA) to pursue harassing actions seemingly designed to 'muffle' and 'distract.'"
The study found that many organizations have toned down their public communications in the wake of the audits, whether in brochures, on the web, public statements or elsewhere.
"There's definitely more caution going on," Kirkby said in an interview from his home in Vancouver.
"It's hurting us. It's not about what this is doing to the charities. It's about what this is doing to what we need in society, which is vigorous policy debates about important issues that we face."
The 16 leaders he interviewed represent a broad range of subject areas, from environment and international development, to social services, research and conservation.
"Pervading the data is the presence of strong emotions that ... highlight a strong sense of confusion, fear, and vulnerability," he wrote in the study entitled "An Uncharitable Chill."
"There is evidence that three specific charitable sectors are being singled out for CRA attention — environmental, development and human rights, and charities receiving donations from labour unions."
Kirkby said some organizations are contemplating joint legal action, such as a lawsuit. Many are also paying closer attention to the internal tracking systems that record whenever they engage in political activity, to ensure the 10 per cent limit is respected to the letter.
And some are creating non-charity, non-profit arms to handle political activity, insulating them from charity audits, he found.
"It says something about the health of our democracy when these moderate organizations who many people donate to and support, peaceful organizations, are demonized ... as being criminal or terrorist organizations ... and then find themselves under threat of audits," he said in an interview.
Follow @DeanBeeby on Twitter