TEHRAN, Young Journalists Club (YJC) - Puigdemont fled to Belgium shortly after declaring Catalonia independent from Spain in October, a move considered illegal under Spanish law.
He faces charges including rebellion and sedition if he returns to Spain but he is the separatists' candidate to lead the region.
The row over Puigdemont's candidacy will come to a head on Tuesday when the Catalan parliament plans to vote on it.
"The government must use every tool made available by the laws and the constitution to make sure that a fugitive cannot be sworn in and become the head of the regional government," deputy prime minister Soraya Saenz de Santamaria said after announcing the appeal to Spain's top court.
Puigdemont reacted immediately. "They are panicking in the face of the will of the people," he said on Twitter.
The newly elected speaker of the Catalan parliament, Roger Torrent, nominated Puigdemont on Monday as the sole candidate for regional leader, against warnings by Madrid that he couldn't take the position.
Puigdemont has not ruled out travelling to Barcelona to take part in the parliamentary vote but has not said he would do it either.
The government's decision to appeal directly to the constitutional court comes after the Council of State - the supreme consultative council of the Spanish government which advises on serious issues - advised against it on Thursday.