The central government has also started proceedings against the 712 of Catalonia's 948 mayors who have offered the use of public spaces in their towns as voting stations.
In a boost for the credibility of the referendum, the mayor of Barcelona said earlier on Thursday that the vote would go ahead in the city, having previously expressed concern that civil servants involved may lose their jobs.
Finance Minister Cristóbal Montoro said a mechanism had been approved for the state to take control of the autonomous region's finances.
Meanwhile, Spain's finance minister has said the central government has made a decision to take over payments of essential services in Catalonia.
Speaking to Telecinco private channel, the vice president of the Spanish Government, Soraya Saenz de Santamaria, recalled that all acts in the October 1 controversial secessionist consultation are banned by Spanish justice.
He said the arrangement implied "political control that is not related to the objectives of budget stability or to the purposes of state legislation in this matter".
Catalonia, an industrial region with a strong export sector and a thriving tourist destination, produces about a fifth of the country's total economic output but complains it receives a lot less back. Once again this week, Rajoy has rejected sanctioning a self-determination vote, telling reporters "there cannot be a referendum and it would be an absolutely illegal act".
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"Right now, we have no idea where they are", he said.
Jose Manuel Maza said that any of the municipal leaders who agreed to help stage next month's vote should be arrested if they fail to appear.
The letter asks for a "political dialogue to be opened, based on the legitimacy that each of us represents, to make something possible that in a democracy is never a problem, and much less a crime: listening to the voice of the people".
Two new laws passed by the Catalan assembly paving the way for the vote have been suspended while state judges consider whether holding it would breach Spain's constitution, which says the country is indivisible.
The signatories also accused the Spanish administration, lead by Mr Rajoy of having gone "on the offensive with unprecedented repression".
Anti-secession sentiment is being supported at the EU level as well, with European Union officials warning that even if Catalonia did successfully secede, it wouldn't mean they'd become members of the European Union.
Although polls show less than half of Catalonia's 5.5 million voters want self-rule, most in the wealthy northeastern region want the chance to vote on the issue, causing unease that is beginning to be felt in financial markets.