The arrests were made during a joint operation with French and Spanish police in the south and southwest of France, the ministry said in a statement.
A total of 16 people were killed when a van drove into crowds on the popular Las Ramblas boulevard in the heart of Barcelona and in a knife attack in the nearby resort of Cambrils in August 2017.
The three arrested were suspected to have links with Moroccan national Driss Oukabir, who was alleged to have rented the van used in the Barcelona rampage.
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