Prime Minister Justin Trudeau says Canada's other vaccine supplier has to cut back on its deliveries next week.
Moderna will ship only about three-quarters of the expected supply, cutting Canada's next shipment by more than 50,000 doses.
Similar cuts are being made to Europe's deliveries, with Italy, France and Switzerland all reporting they, too, are getting less than 80 per cent of their expected doses.
It is more bad news for Canada's already troubled vaccine supplies, after Pfizer cut back its deliveries by more than two-thirds since mid-January.
Pfizer is also pushing Canada to change the label on its vaccine to declare each vial contains six doses, instead of five, allowing the drugmaker to meet its delivery contract by sending fewer vials.
However Trudeau says new export controls Europe is imposing on COVID-19 vaccines produced there won't affect Canada, and he expects Pfizer and Moderna to catch up on their deliveries before long.
European Commission President Ursula von der Leyen said Friday the commission is following through on a threat to force COVID-19 vaccine makers to show them what vaccines they are producing in Europe and where those are going.
She said the export transparency rule is temporary but has to be done as the continent is in an ongoing battle with vaccine-makers about slow deliveries.
Both Pfizer-BioNTech and AstraZeneca are behind on their scheduled deliveries to European nations, but it is the latter with which Europe is having the loudest fight, demanding the company ship doses made in the United Kingdom to make up for shortfalls due to production issues in its European plants.
Trudeau spoke with von der Leyen earlier this week and he said she told him Canada's deliveries would continue. International Trade Minister Mary Ng spoke Thursday with European trade commissioner Valdis Dombrovskis, and said he reiterated that assurance.
The delivery news will overshadow Friday's positive vaccine development with American pharmaceutical giant Johnson and Johnson reporting its vaccine is very good at preventing people from being hospitalized or dying from COVID-19.
The vaccine is the first to use just a single dose and can be stored in a fridge for up to three months, making it a potential game-changer in the COVID-19 vaccination campaign.
The results aren't quite as good as those seen in the two vaccines Health Canada has already approved, with both Pfizer-BioNTech and Moderna saying their vaccines showed 95 per cent efficacy against severe illness.
Johnson and Johnson says its single-dose vaccine is 85 per cent effective against severe illness a month after the injection is given, and 66 per cent effective against both moderate and severe illness.
The federal government has already pre-purchased 10 million doses of the vaccine, but it is still being reviewed by Health Canada.
There is no timeline yet for when approval might come or when those doses would be delivered for use in Canada.