Others implicated include Catalan parliament speaker Carme Forcadell and senior lawmakers from the region, a court spokesman said, Independent reported.
A total of six people face possible charges of rebellion, sedition and embezzlement.
Mr. Puigdemont was at the head of the separatist push that saw deputies vote for independence last Friday after a tense week of negotiation and brinkmanship between Madrid and Barcelona.
It followed 1 October's disputed referendum that had been deemed unlawful by Spain's constitutional court.
A majority voted for secession but turnout was greatly reduced after a crackdown by Madrid.
Huge numbers of Catalans favor unity with Spain and Barcelona has seen large demonstrations in support of remaining part of the whole.
Mr. Puigdemont and others face, potentially, decades in prison if convicted of rebellion.
Following the vote Spain's senate voted to grant Prime Minister Mariano Rajoy new powers under article 155 of the constitution.
Mr. Rajoy quickly sacked the Catalan government and ordered new elections on 21 December, promising to "restore legality" to the region.