One 49-year-old woman in Austria died from “severe coagulation disorders”, and a pulmonary embolism put another in the hospital.
Health authorities have now launched an investigation into the reports and vaccine.
The suspension marks another setback for the European vaccination rollout that is only now beginning to stutter to life after a delayed start.
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The agency added fears may have come from one particular batch but ruled potential defects “unlikely”.
The EMA added: “Batch ABV5300 was delivered to 17 EU countries1 and comprises 1 million doses of the vaccine.”
“Some EU countries have also subsequently suspended this batch as a precautionary measure, while a full investigation is ongoing.
“Although a quality defect is considered unlikely at this stage, the batch quality is being investigated.”
The UK became the first country to approve the AstraZeneca jab, developed by researchers at Oxford University, earlier this year.
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The firm said: “An analysis of our safety data of more than 10 million records has shown no evidence of an increased risk of pulmonary embolism or deep vein thrombosis in any defined age group, gender, batch or in any particular country with COVID-19 vaccine AstraZeneca.
“In fact, the observed number of these types of events are significantly lower in those vaccinated than what would be expected among the general population.”
AstraZeneca added incidence of clotting-related disorders was lower in the people they tested compared to the general populace.
The EU’s Pharmacovigilance Risk Assessment Committee (PRAC) has taken charge of investigating the jab.
The committee will assess the batch and any potential “thromboembolic events” associated with it.