Another leading citizens' agency, the Federation of Barcelona Neighbours, called on people to take to the streets in defence of Catalonia's institutions.
So far the crisis has been peaceful but police scuffled with Catalan demonstrators this week. Carles Puigdemont, head of Catalonia's pro-sovereignty government, accuses the Spanish government of trying to prevent a vote on independence, suspending their autonomy.
In the early hours of the morning, armed officers from the Guardia Civil arrived at ministries, including the offices of economic affairs, foreign relations and the social affairs, said the spokesman.
Mr Rajoy said the regional government had been warned that they were destroying Spain's national sovereignty, "There's no democratic state in the world that would accept what these people are planning", he said.
A leading editor has said the Spanish and Catalan governments are headed for a major clash as the ongoing row of independence grows.
With tensions mounting, separatist organisations called for more people to protest as leaders in a region deeply divided over independence pressed ahead with preparations for the October 1 vote.
"Spain has de facto suspended the self-government of Catalonia and has applied a de facto state of emergency", he said. The Spanish government has vowed to stop the vote, which it says is unconstitutional, and the two governments - one in Madrid, one in Barcelona - are now on a collision course. Officials said 80% of them backed independence. The Catalan Parliament this month legislated for the referendum and approved the foundations for a Catalan republic in defiance of Spain's Constitutional Court.
Among those arrested on September 20 was Josep Maria Jove, secretary general of economic affairs and Catalonia's deputy vice president, a regional government spokesman said.
However, his government's heavy-handed approach has only stoked the fires of those seeking independence for Catalonia.
"It is obvious that the rules of the game have been changed", Catalan vice president Oriol Junqueras told Catalonia's TV3 a day after police detained 14 Catalan officials suspected of preparing the vote slated for October 1.