At Holyrood, Mr Matheson said ministers had contacted the Spanish Government and added that External Affairs Secretary Fiona Hyslop is to write to the Spanish ambassador following the issue of a European Arrest Warrant for St Andrews University academic Professor Clara Ponsati.
The Scottish Government has also pledged to raise concerns with how European Arrest Warrants are being used with the European Commission.
Mr Matheson said: “We have today been in touch with the Spanish embassy and the Cabinet Secretary for Culture Tourism and External Affairs is writing to the Spanish ambassador to express the Scottish Government’s regret at the issuing of a European arrest warrant to members of the former Catalan government and re-elected members of the Catalan parliament. The fact that our justice system is legally obliged to follow due process in the determination of extradition requests does not change those views.”
The Justice Secretary went on to remind MSPs that case of Professor Ponsati, the former Catalan education minister who is expected to hand herself into Police Scotland this week, is “sub-judice”.
He said Scottish ministers were unable intervene in European Arrest Warrants saying extradition decisions were a matter for the courts.
But he said ministers had concerns about the European Arrest Warrant process.
He added: “I can inform the chamber and the member we do have concerns over how the system of European Arrest warrants is being used and we will be raising this matter with the European Commission.”