The Catalan regional government confirmed Josep Maria Jove, secretary general of economic affairs, was among those arrested.
According to El Pais newspaper, 14 people in total have been arrested.
Puigdemont reiterated his call for Catalans to "defend democracy" and to vote en masse in the referendum.
The raids came after the local government vowed to continue with an October 1 referendum on Catalonia's independence, a vote Madrid says is illegal and unconstitutional. While Catalonia is one of Spain's wealthiest regions, Catalans argue they pay more into the national budget than they get back.
But Madrid is against it, pointing to the constitution which states that the unity of the Spanish nation is "unbreakable" and that only the central government has the power to call a referendum on any matter.
On June 9, the president of the autonomous region, Carles Puigdemont, said that Catalonia would hold a unilateral referendum on independence on October 1, 2017, prompting criticism and objections from Madrid.
Spain's government intensified its crackdown on Catalan separatists, raiding offices and arresting nine officials on Wednesday, and investors took it in their stride.
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On Tuesday, Spanish police seized almost 50,000 envelopes with the Catalan government's logo from a delivery company, which were going to be used to deliver ballot materials. On Sept. 19, for example, the mayors of three Catalan municipalities who pledged to cooperate with referendum organizing efforts were summoned to testify before the prosecutor's office in Barcelona.
The Guardia Civil searched several regional government headquarters in Barcelona, a Catalan government spokesman said.
The Spanish government has increased its suppression of the independence vote that included the arrests of a dozen regional officials today and the seizure of 10 million ballot papers.
Spanish police working to halt a contentious independence referendum in the northeastern region of Catalonia have seized nearly 10 million voting slips at a warehouse in a Barcelona suburb, the Interior Ministry said on Wednesday.
With the latest measure, virtually all Catalan spending will be in the hands of Madrid.
Catalonia, which represents a fifth of Spain's 1.1-trillion-euro economy, has some 900 mayors.
Hundreds gathered outside government offices in Barcelona to protest the crack-down, chanting "We will vote", Reuters reported. Both officials declined to be identified by name, following internal protocol.