Judge Carmen Lamela of the National Court, which deals with high-profile political and financial cases, said in her ruling there was evidence that former Mossos d'Esquadra chief Josep Lluis Trapero was part of a “criminal organisation” that sought to break Catalonia away from Spain.
The judge also slapped sedition charges on two other top officials with the regional police force, as well as an official with the Catalan interior ministry.
Conviction could carry a prison sentence of up to 15 years.
Lamela said Trapero and the three others carried out a “premeditated strategy that was perfectly coordinated” to help achieve secession during the lead-up to a banned independence referendum in Catalonia on October 1st and the day of the vote itself.
The judge also said Catalan regional police did not respond to requests for aid made by officers from Spain's Guardia Civil force who were searching a Catalan government building in Barcelona on September 20 as part of a probe into preparations for the banned referendum.
- The Puigdemont files: What you need to know about the case
- WATCH: Angry protest in Barcelona after ex-Catalan leader arrested
- Catalan separatists face rebellion charge as another key figure flees abroad
The Guardia Civil officers were not able to leave the building because thousands of pro-independence demonstrators were gathered outside.
Trapero exchanged 17 telephone calls that day with one of the organisers of the demonstration, Jordi Sanchez, the head at the time of the powerful grassroots pro-independence group ANC, the judge said in her ruling.
Catalan regional police also did not take steps to stop the referendum from going ahead as ordered by the courts, she added.
Catalan regional police officers showed up at polling stations in some cases three hours later than scheduled while others did not seize ballot boxes until after voting had ended, the judge said in her ruling.
Some Catalan regional police officers were ordered to monitor the movements of Spanish national police on the day of the referendum, she added.
Spain's central government dismissed Trapero on October 28th, a day after it imposed direct control on the region over its independence bid.
Llamela was charged with investigating the role of the Mossos d'Esquadra in the independence push.
Spain's Supreme Court judge Pablo Llarena, meanwhile, is in charge of investigating the role played by Catalonia's separatist leaders.
He has ruled that some of them will be tried for “rebellion”, an even more serious charge that carries a jail term of up to 30 years.