The problem has led to the postponement of some operations throughout the province.
"There is no contamination of the blood in Quebec," Health Minister Rejean Hebert told reporters in Quebec City.
''There is a problem with some batches of blood that could be contaminated and we have withdrawn those batches of blood to be sure there's no problem."
Hebert insisted there is no risk to patients, adding that the agency, Hema-Quebec, has the reserves necessary to fulfil the needs of hospitals.
A Montreal health services spokeswoman said some elective surgeries at five area hospitals were delayed, including heart operations at three major Montreal hospitals.
A spokesman for Hema-Quebec said there was a problem with the equipment used to collect blood. Tiny cracks were found in some packaging used to store blood stock at a Montreal holding facility.
Laurent-Paul Menard said the blood, some of which had already been distributed to hospitals, risked being exposed to air, which creates favourable conditions for bacteria.
Menard said about 70 per cent of the agency's stock might be held for examination.
Hema-Quebec suggested the leaks in the bags appeared to have been a manufacturing defect.