Malta is one of three countries which has opted out of the EU's new defence and security cooperation.
Denmark, the UK and Malta opted out of the agreement which lays the foundation for a proposed European defence union.
Since certain operations of the new entity might be in breach of the neutrality clause of Malta's constitution, the government decided to take a step back, sources told Times of Malta.
"Once the operation is up-and-running, the government might revisit its decision. At this stage we decided to err on the side of caution," the sources said.
The decision by EU foreign ministers allows closer EU-level security cooperation and military capacity building, which is meant to make the EU less dependent on the US for its security needs.
Participation in the so-called Permanent Structured Cooperation (PESCO) is voluntary for the EU's 28 member states.
The cooperation will begin with 17 concrete projects, which include establishing a medical unit, a logistics hub, a centre for training missions and the development of common standards for military radio communication.
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