The Spanish government has called a meeting for Monday to discuss what action to take after the crowd loudly jeered during the national anthem at the final between Barcelona and Athletic Bilbao.
A capacity crowd of 99,000 supporters filled Barca's Camp Nou stadium Saturday for the Catalans 3-1 victory, but the game had a controversial beginning as supporters of both clubs with a strong regional identity drowned out the traditional playing of the anthem with whistles.
"The government condemns the attacks against symbols which represent all Spaniards, the democracy that protects us and the society we share," the government's press department said in a statement.
"As a consequence the state commission against violence, racism, xenophobia and intolerance has been called for this Monday, June 1, with the objective to proceed with charges for these actions."
A letter had been sent to both clubs and the Spanish Football Federation ahead of the final by the president of the country's sports council warning that punishment would be forthcoming if the playing of the anthem was not respected.
It is the third time that Barca and Athletic have met in the final in the past seven years with a similar reaction having taken place in the previous finals in Valencia in 2009 and Madrid in 2012.
In contrast to the multinational nature of modern football, Athletic maintain a policy of only playing Basque born or trained players.
Meanwhile, Barca's success on the field has made them a strong symbol for the Catalan independence drive.
Earlier this season Barca got special dispensation to wear their away shirt in the colours of the Catalan flag in a home game against Athletic to mark the 300th anniversary of the loss of Catalan sovereignty.