The latest spike in tensions between the wealthy Spanish region and the central government comes as jitters continue in Europe following Britain's shock vote to leave the European Union.
"This threat is very serious and affects the essence of democracy: stopping access to polling stations," Neus Munte, spokeswoman for the Catalan government, told regional radio RAC1.
Catalonia's government decided last year to hold a Scotland-style binding referendum for independence this September - a move ratified in a resolution voted by the majority separatist, regional parliament.
But Madrid insists any such vote would be illegal and Spain's Consitutional Court has suspended the resolution.
Conservative Prime Minister Mariano Rajoy is determined to stop a referendum from happening, saying he is against any move that threatens Spain's unity.
According to media reports in Spain's main dailies on Thursday, Madrid is considering drastic measures, such as closing public schools where polling booths are normally set up or taking control of Catalan police, which is normally managed by the regional government.
In a press briefing, Spain's Deputy Prime Minister Soraya Saenz de Santamaria refused to comment on the allegations, merely calling for "dialogue."
The war of words comes ahead of the high-profile trial Monday of former Catalan president Artur Mas, over a previous contested referendum initiative.
Mas and two former members of his government will be in court over their role in staging a symbolic, non-binding independence referendum in 2014 despite it having been banned.
More than 80 percent of those who cast their ballot did so for independence - although just 2.3 million people out of a total of 6.3 million eligible voters took part.
Accused of serious civil disobedience, Mas faces a 10-year ban on holding public office, as do his two former associates.
Faced with their possible conviction, Munte hinted earlier this week that the referendum could be brought forward as a form of retaliation.
"We are living through very exceptional circumstances... and the timeframe could be re-assessed," she said.
Catalans have nurtured a separate identity for centuries, with their own language and customs.
Their long-standing demands for greater autonomy were exacerbated during Spain's recent economic crisis, leaving many resenting the amount of taxes they pay to the central government in Madrid to subsidise poorer regions.