It is the latest in a series of blows for the French company, after the UK pulled out of a £1.2 billion deal for 100 million doses in September.
Valneva did not comment on how the latest development may affect employees at the West Lothian site.
Following the UK’s decision to drop its order, Valneva announced an advance purchase agreement with the European Commission in November.
This would see 24 million doses delivered in the second and third quarters of 2022, with the option to purchase a further 36 million to be delivered in 2023.
But the European Commission has told Valneva it intends to scrap this deal, which was dependent on the company’s vaccine being authorised by the European Medicines Agency (EMA) by April 30.
Valneva now has until June 12 to get this authorisation or come up with an alternative plan. The company has said it will work with the European Commission on resolving the issue.
It has also begun speaking to individual European member states who may still want to buy the vaccine, chief executive Thomas Lingelbach said.
It comes after Valneva’s vaccine was authorised by the Medicines and Healthcare products Regulatory Agency (MHRA) in the UK on April 14.
It has also been authorised in Bahrain and the United Arab Emirates.
If the agreement with the European Commission is scrapped, Valneva will not be required to return the down payments it has already received.
Mr Lingelbach said the news was “regrettable”.
"The EC decision is regrettable, especially as we continue to receive messages from Europeans who are looking for a more traditional vaccine solution,” he said.
"We have started a dialogue with member states who are interested in our inactivated approach. Valneva continues to believe that its vaccine candidate VLA2001 can make an important contribution to the fight against Covid-19 and complement existing vaccines with an inactivated, whole virus approach”.
Valneva’s product, an inactivated whole virus vaccine, is a more traditional approach than some other vaccine candidates.
The company has said it will be suitable for use for particularly vulnerable patients, as well as for boosters and new variants.
In September the UK Government terminated an order for 100 million doses of the vaccine, citing a breach of obligations on Valneva’s part which the company “strenuously” denied.
Health secretary Sajid Javid told Livingston SNP MP Hannah Bardell that Valneva’s vaccine “would not get approval by the MHRA”.
The vaccine gained MHRA approval in April.
The Scottish Government said it would discuss ways to support Valneva and the Livingston site following the UK withdrawal, including considering breaking away from the four-nation vaccine procurement process in place so far through the pandemic to do business directly with Valneva.
In February it awarded a research and development grant of up to £20m to Valneva through Scottish Enterprise.
Announcing the funding package, business minister Ivan McKee called the Livingston factory an “important asset” to Scotland, and Valneva a “valued contributor to our life sciences sector”.