Elite soldiers involved in Canada’s most dangerous and secretive military operations could now lose a special monthly allowance if they are sick or injured for more than 180 days, CTV News has learned.

The Department of National Defence quietly rolled out the policy in September.

The new rules mean that personnel with the Canadian Special Operations Forces -- many of whom work on top-secret missions across the globe -- will lose the special compensation if illness or injury restricts their duties for more than 180 days.

Paratroopers, submarine crews, pilots and air crews, rescue technicians and ships’ crews are also among the affected.

Sources tell CTV News the Department of National Defence is now enforcing the policy, and pay is being clawed back with little warning.

But those most affected by the controversial policy can't speak publicly because their identities remain secret. Some have told CTV’s Mercedes Stephenson that they're frustrated and don't understand why they are taking a financial hit over temporary injuries.

The Canadian Forces is defending the new rules and says the pay in question is linked to specific duties that troops must be able to perform to qualify.

Lieutenant-General Charles Lamarre said the policy is “a question of fairness.”

“But we still want to give them a good period of time in which they can get better in roughly half a year,” Lamarre said. “And if they can't, that allowance will be removed.”

Critics say the policy could place undue stress on soldiers, who may feel pressured to hide their injuries or rush back to work before they are better.

Conservative defence critic James Bezan called the move hypocritical as the Liberal government says it’s prioritizing mental health.

“They are again saying one thing and doing another that undermines not only the Canadian Armed Forces, but the health of our soldiers,” Bezan said.

The new policy could translate to a loss of more than $23,000 in pay over six months for a JTF-2 assaulter.

Chris Dupee, a veteran who has struggled with post-traumatic stress disorder, says he understands the government’s position.

“I get both sides. I understand the economics of taking away the allowance if you're not deployable I get all that,” he said.

But he also knows that losing the monthly allowance is a hard blow to military families.

“That's a big chunk taken out of your family income that you've grown used to,” Dupee said.

Dupee worries that soldiers who require time to recover may be counting down the days they have left to get back on the job, even if they’re not ready.

“That's a clock that's ticking. That's something that's going to be constantly embedded into that individual's mind, right? And that's going to be a huge stress,” he said.

Former Special Forces Commander Steve Day said the policy will have serious consequences on the forces.

“It will become a morale issue and without a doubt it will affect retention,” Day said.

“We may unfortunately start seeing soldiers and sailors, air men and air women, hiding their injuries if they know that potentially some of their financial compensation is at risk.”

With a report from CTV’s Mercedes Stephenson in Ottawa