But with a June 30 deadline looming on the proposed changes, the department realized that's exactly how the new rules would apply - and officials were forced to get cabinet approval for an amendment.
The approval came through only at the last minute: the order-in-council making the change was signed on June 28 and published Tuesday.
The policy - which strips refugee claimants of access to pharmaceutical, dental and vision coverage and limits other forms of coverage - had been announced in April.
It's projected to save the government $20 million a year for the next five years. At the time, the Conservatives said the changes were meant to ensure refugee claimants didn't get better health benefits than average Canadians.
But the change was met by immediate and sustained criticism from advocacy groups who accused the Conservatives of denying care to some of the most vulnerable in Canadian society.
That included refugees brought over by Canada through its international obligations, known as government-assisted refugees. About 7,500 come to Canada each year.
The Conservatives were resolute in the face of the criticism, insisting the changes were warranted.
They stuck by that on Tuesday.
"Our intention was to ensure that those who come to Canada as asylum seekers from abroad do not receive better health-care coverage than Canadians," said Alexis Pavlich, a spokeswoman for the immigration minister.
"Our intention was never to have this policy impact government-sponsored refugees who have been living in UN refugee camps, who arrive in Canada as permanent residents, but who do not initially qualify for provincial social support."
The original policy had divided refugee claimants into two groups based on the status of their claim and country of origin. Neither would receive extended benefits.
Those whose claim is rejected or who are from a yet-to-be defined list of countries would only receive health care if there was a public health or safety risk.
The government has since amended the policy to provide for a third group of refugee claimants who are covered by a federal program that provides financial and other assistance.
They will receive the extended benefits as long as they are covered by that program.
Kenney's office insisted the government was clear from the outset that government-assisted refugees weren't affected by the cuts.
But doctors who had protested the cuts claimed the change as a victory Tuesday.
It's still too little, too late, they said.
"The vast majority of refugees who are sponsored by church groups and other citizens will lose access to life-saving medications," said Dr. Megan Williams, an Ottawa physician.
"Many of these refugees come from refugee camps and have endured war and other forms of violence. Imposing these cuts is inhumane for refugees and unfair to the church groups and other citizens who have sponsored these refugees in good faith."
The official change to the policy was required because of an earlier bureaucratic switch which saw government-assisted refugees being processed as privately sponsored refugees in order to get them to Canada faster.
The result was to place their benefits at risk.
"The original criteria did not make this intention clear which is why the language of the policy has been modified," Pavlich said.