Carles Puigdemont fled to Belgium after Madrid imposed direct rule on Catalonia following a unilateral declaration of independence in October last year. He is facing imprisonment in Spain if he returns home for his role in the region's independence bid.
"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 and his allies say that he could govern from abroad, winning him the nickname the hologram president.
"They are panicking in the face of the will of the people," Puigdemont tweeted in an immediate reaction to the appeal.
The Catalan parliament on Monday nominated Puigdemont to rule the region in defiance to Madrid.
It will vote on his candidacy on January 30.
Spain’s deputy prime minister said that if the court agreed with the government, Puigdemont's candidacy would be invalidated and the vote could be suspended.
But, the Catalan separatists last year defied the court's decision banning a referendum on Catalonia's secession and held it anyway.