It said the demonstrators cut the AP7 motorway at La Jonquera near the city of Gerona in eastern Spain as well as the N-II road near the border.
The action followed a fourth night of violence in Barcelona, in which the separatists burned barricades and clashed with police.
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Hundreds of young protesters chanting “independence” set fire to improvised roadblocks in the centre of the city late Thursday, tossing Molotov cocktails at police, who responded by firing foam and anti-riot rounds, according to AFP correspondents.
The separatists have called a general strike and a mass rally on Friday against the Supreme Court's decision to jail nine of the separatist leaders for their role in a referendum banned by Madrid and a short-lived declaration of independence.
The court's decision has thrust the Catalan dispute to the heart of the political debate ahead of Spain's November 10 general election, its fourth in as many years.