"The public prosecutor's office will take the appropriate legal actions in the High Court of Justice of Catalonia," the public prosecutor's office said in a statement.
The Catalan government says 2.3 million people took part in the vote on November 9 which Mas held following a legal block by the central government against his plans to hold an official, non-binding referendum on the issue that day.
The ballot was organised by over 41,000 volunteers with voting stations set up in town halls and schools across the wealthy northeastern region.
Prosecutors have not yet decided which crimes Mas will be accused of but Spain's Attorney General Eduardo Torres-Dulce has said he could be charged with: civil disobedience, abuse of power, usurpation of duties and embezzlement of public funds.
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If Mas is found guilty of civil disobedience or abuse of power it could eventually mean that he would be banned from standing for public office for several years.
A sentence for embezzlement of public funds could lead to a jail term of between three and six years.
The attorney general on Monday asked public prosecutors in Catalonia to launch a lawsuit against Mas but they refused, arguing they lacked arguments to pursue a case against the Catalan president.
The deputy secretary of Spain's ruling conservative Popular Party, Carlos Floriano, accused Catalan prosecutors of being "contaminated by the nationalists' atmosphere".
The attorney general then met with a special commission of 27 public prosecutors from across the country yesterday as required by law and they overwhelmingly recommended that the lawsuit against Mas and the other Catalan government officials be launched.
Mas has hailed the ballot as a "total success" but Spanish Prime Minister Mariano Rajoy has dismissed it as a "deep failure" since "two out of three Catalans paid no attention".