"It is absolutely inappropriate that they [Catalan authorities] strive for the declaration of independence to come into effect on the next day or that it would be a postponed declaration of independence", the prime minister said.
When will it be declared?
He added: "I want to say something with absolute clarity - while the threat of independence is in the political landscape, it will be very hard for the government to not take these decisions".
Recent polls had indicated that Catalans are split on independence, though leaders said the violence during the referendum turned many against the state authorities.
If Catalonia were to declare independence "it would be like cutting off an arm", he told AFP, saying there was "a lot of concern" about the government's perceived lack of action to resolve the crisis.
But the Catalan government has not provided details regarding what means it has to assume the classic duties of a state such as border controls and defence.
Catalan President Carles Puigdemont is expected to address the regional parliament on Tuesday.
Rajoy also said he planned to leave in Catalonia the extra 4,000 police officers the government had shipped in to region for an independence vote on October 1 until the crisis was over.
Caroline Gray, Lecturer in Politics and Spanish at UK-based Aston University also predicts further tensions between Spanish government and Catalonia in case of independence declaration.
Catalonia's referendum law establishes an "exceptional legal regime" that "prevails hierarchically overall norms which it may conflict with", meaning it overrides other laws.
He did not rule out suspending Catalonia's regional autonomy - a move that could risk sparking unrest.
The demonstrator said it is hard to get hundreds of thousands of people out on the streets if a political party or major organization is not behind the call. "Here they are always with their doors open for dialogue, but I think this will end badly", he said.
The European Union has warned that an independent Catalonia would be left outside of the bloc.
On Friday, Catalonia's police chief and two prominent separatist leaders including Cuixart avoided being remanded in custody at a court hearing over sedition accusations.
This led to accusations of hypocrisy voiced against the European Union, with Serbian President Aleksandar Vucic saying: "How come that in the case of Catalonia the referendum on independence is not valid, while in the case of Kosovo, secession [from Serbia in 2008] is allowed even without a referendum?" .
Meanwhile, Catalan foreign affairs chief Raül Romeva told the BBC his government would go ahead with an independence debate in parliament.
Puigdemont, a lifelong separatist, became president of Catalonia in January 2016.
But something like a precedent for this exists from the Scottish referendum of 2014 - which was held with London's blessing - and it is not promising for Catalan separatists. The police crackdown on the independence referendum in the affluent Spanish region led to over 800 people being injured and mass protests, with 700,000 people taking to the streets of Barcelona to vent their anger and voice support for the local authorities.