In a televised announcement, Carles Puigdemont said Madrid was failing to respect the rule of law after Prime Minister Mariano Rajoy announced he would move to dismiss Catalonia's separatist executive, take control of regional ministries and call elections.
It does not suspend the autonomy of Catalonia, which is guaranteed in Spain's constitution and the Statute of Autonomy, but it allows the government to take special measures to force the region to adhere to its constitutional obligations.
The State Attorney General José Manuel Maza confirmed on Saturday that "a complaint is being prepared for rebellion" against the President of the Generalitat of Catalonia, Carles Puigdemont, and other independence leaders.
Regional authorities said about 90 percent of those who cast ballots voted for independence. The specific measures need approval from the country's Senate.
It has never before been invoked in democratic Spain.
Spain's National Security Department said late on Friday that an undisclosed number of government websites had been hit in recent weeks with slogans supporting independence for the country's Catalonia region. The article is only two paragraphs long and does not outline rules for implementation.
"And at the same time we need to return to institutional normality".
In a significant upping of the stakes in his bid to rein in the region's pro-independence rulers, Mr Rajoy has said that although the Catalan parliament will not be dissolved immediately, its functions will be limited to "avoid measures contrary to the Constitution". The referendum has been deemed illegal by the central Spanish authorities.
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It is also strongly rumoured the Nationalist coalition will vote for Catalonia to break away from Spain in Parliament next Friday, the same day that Madrid's measures are expected to be confirmed by the Senate.
El Pais, the Spanish newspaper, reports that the government will have the ability to take control of TV3, the primary television channel of Catalan public broadcaster Televisió de Catalunya, "to ensure the transmission of 'truthful and objective information balanced".
During the meeting, which started around 10:00 am (0800 GMT), Prime Minister Mariano Rajoy and his ministers will decide on what powers to take away from the wealthy region, which now enjoys wide autonomy including control over its own policing, education and healthcare.
The president of Barcelona FC, one of the world's best-known symbols of Catalan identity, threw his weight behind the region's institutions.
In his message, Putteman said that the suspension of the Declaration of independence, an Autonomous community of Spain "remains in force".
Almost 1,200 companies based in Catalonia have re-registered in other parts of Spain since the referendum and and Spain this week cut its national growth forecast for 2018 from 2.6 per cent to 2.3 per cent.
Although Mr Rajoy underlined he had the support of both the Socialist Party and Ciudadanos, Spain's fourth largest political grouping, the measures were described as "authoritarian and a botched job." by the left-wing Podemos coalition.