Police on Wednesday managed to disperse Catalan separatist protesters from a busy motorway linking Spain and France, reopening the road in both directions after more than 48 hours of intermittent blockages.

The demonstration caused chaos on an artery which is particularly important for cross-border freight transport and is used by some 20,000 lorries per day.

The highway jam began on Monday morning when hundreds of activists flocked to the border area of La Jonquera, blocking the busy AP7 motorway linking northeastern Spain and southern France.

The busy cross-border motorway linking Spain and France suffered intermittent blockages for more than 48 hours The busy cross-border motorway linking Spain and France suffered intermittent blockages for more than 48 hours Photo: AFP / LLUIS GENE

Organised by activist group Democratic Tsunami, it was just the latest operation in an ongoing campaign of protest that began in mid-October when Spain's top court jailed nine separatist leaders over a failed 2017 independence bid.

Although the blockage was briefly cleared by French and Spanish police on Tuesday morning, protesters shifted their action some 65 kilometres (40 miles) further south, where the motorway passes through the city of Girona.

With the motorway impassable, many cars and trucks were stuck there overnight.

IMAGES Protesters with the pro-independence movement block roads in Barcelona, causing traffic to come to a standstill. On Monday, hundreds of separatists shut down the busy motorway between France and Spain at the border in protest over the sentencing la IMAGES Protesters with the pro-independence movement block roads in Barcelona, causing traffic to come to a standstill. On Monday, hundreds of separatists shut down the busy motorway between France and Spain at the border in protest over the sentencing last month of nine of their leaders to lengthy jail terms. Photo: AFPTV / Anahi ARADAS

Also Tuesday, demonstrators blocked another cross-border motorway in Irun, at the other end of the Pyrenees, linking Spain's Basque country with southwestern France, calling their protest "Operation Snail".

By Wednesday morning, clashes broke out at the Girona site where masked protesters torched barricades and hurled stones at the security forces who eventually managed to disperse them, the Catalan regional police said.

Its leaders remain unknown and they keep in touch with each other through encrypted messaging apps such as Wire.

The protests were also backed by activists from the radical CDR, which has also vowed to continue its direct action.

"As long as there are hostages... and we do not have the right to self-determination, there will be chaos. Independence or barbarism!" it tweeted on Wednesday.