Given the escalated situation, Ramón Espinar Podemos, a social activist and politician with the Podemos political party, said from the protest in Madrid that "we're no longer discussing whether Catalonia has independence".
The first minister went on to suggest the treaty between the United Kingdom government and Scottish government for the legal 2014 independence referendum, known as the Edinburgh Agreement, was the best course of action in Spain.
In a televised statement on Wednesday evening, Rajoy called on Catalonia's separatist leaders to "stop this escalation of radicalism and disobedience once and for all".
Rajoy retorted that the referendum was "radically undemocratic" and asked separatist leaders to give up their "impossible pipe dream".
"There is still time to avoid bigger problems", he said.
Catalan nationalism has been stirred by Spain's economic crisis. His stance has the backing of most Spanish opposition parties.
Spanish Interior Ministry officials would not identify the arrested regional officials, saying the investigation was ongoing.
Among those detained was Josep Maria Jove, Catalonia's junior economy minister. Jove is No. 2 to the region's vice president and economy chief, Oriol Junqueras. Neither side shows any sign of backing down: Puigdemont says the referendum will go ahead; Rajoy is adamant it won't.
"We will do it because we have contingency plans in place to ensure it happens, but above all because it has the support of the huge majority of the population, who are sick of the arrogance and abuse of the People's Party government".
And a demonstration in support of Catalonia's pro-independence movement is to be held in Glasgow later.
Several thousand Catalans gathered to angrily protest the raids outside government offices in the region's capital, Barcelona.
It is not yet clear whether the police operation would be enough to prevent the vote overall or if it could instead bring fresh momentum to the secession campaign. There were no reports of arrests or injuries. Puigdemont said, "Logically, the state has to react".
Catalan president Carles Puigdemont accused the Spanish state of implementing a "de facto state of emergency" and suspending the region's federal powers by tightening control over Catalan finances.
Madrid has also threatened to arrest local mayors who facilitate the vote.
Catalonia represents a fifth of Spain's 1.1-trillion-euro ($1.32 trillion) economy and enjoys wide self-government authority, although key areas such as infrastructure and taxes are in the hands of central authorities.
Some 7.5 million people live in Spain's well-off north-eastern region and a majority are thought to be in favour of having a vote.
"FC Barcelona, in remaining faithful to its historic commitment to the defense of the nation, to democracy, to free speech, and to self-determination, condemns any any act that may impede the free exercise of these rights", said the release.
"It started peacefully, with some 40,000 protesters singing the Catalan national anthem outside a government building raided by Spanish Civil Guards".