The man arrived in Saskatoon several months ago after fleeing a Middle Eastern country. Soon after arriving, he started having abdominal pain and was diagnosed with cancer.
Saskatchewan Health Minister Dustin Duncan said cancer treatment was started.
"At that time the cancer agency was informed by the federal government that they would not be paying the bill," Duncan told reporters Wednesday.
"It certainly is not in line with what they've told us, (that) coverage would be provided in urgent and needed care. Certainly, I think that would apply in this case, so we were certainly surprised that this didn't meet that test."
Ottawa announced changes in the spring to the Interim Federal Health Program, which provides temporary health coverage for protected persons, refugee claimants and other groups not eligible for provincial health insurance.
Under those changes, some refugee claimants saw cuts to their drug, dental and vision coverage. Additionally, those whose refugee claims are rejected and those from a yet-to-be defined list of "safe" countries will only receive medical care if their condition is deemed a risk to public health or safety.
The federal government said it hopes the changes will deter bogus refugee claims and ensure failed asylum seekers can't take advantage of Canada's free health care.
But Duncan said confusion abounds.
"It is very frustrating, not just how this was left to the provinces by the federal government, but even now many months after the changes were made, there is still a lack of clarity in terms of what they are going to continue to cover," he said.
The province stepped in to cover the man's chemotherapy costs.
The case came to light when the man's plight was raised Wednesday in the Saskatchewan legislature.
New Democrat Cam Broten urged the province to help refugees who lost their coverage because of the federal cuts. Broten said the man in Saskatoon received chemotherapy, but he couldn't afford anti-nausea medication for the side effects.
"In the state of this confusion, while it's a total mess (of) communication between the province and the federal government, people are falling through the cracks and people are suffering," said Broten.
A nun who is helping the man said he doesn't want to be identified because he fears being kicked out of Canada and what may happen to his family in his homeland.
Sister Carol Borreson said the man's first round of chemotherapy was done while he was in the hospital, so the medication was covered. But his second round of chemo was done on an out-patient basis, so medication to help with nausea was not covered.
Borreson said the man was so sick that he had to go to the emergency room for intravenous fluids.
"On a health care system (level), that doesn't make sense," she said.
"On a personal level, it's just awful what happened to that gentleman. He has enough anxiety, concern and worry. I mean I just think that's awful that on top of that he had to deal with all this nausea and vomiting and get to the point where he was not sure whether he would go for the next round of chemotherapy or not."
"His words to me were 'I don't know if I can do that again.' "
Borreson said donations have since been raised to cover the anti-nausea medication for the man, who is on his fourth round of chemo.
At least one province has decided to backfill the federal cuts.
Manitoba said in September that it will help refugees access health benefits the federal government took away. Health Minister Theresa Oswald said the province doesn't agree with the cut because it's hurting families and will lead to longer-term and more expensive problems.
Duncan said Saskatchewan would look at covering the man's anti-nausea medication and would consider other situations on a case-by-case basis.
"I don't, at this point, see backfilling the entire supplementary health benefits that were provided by the federal government as the answer because at this point, frankly, I think it takes the federal government off the hook," he said.