Oriol Junqueras, who was sacked as vice-president when the Catalan parliament declared independence on October 27th, Joaquim Forn, who used to be in charge of interior matters in Catalonia, and the leaders of two pro-independence associations will stay in prison, the court said.
Six other former ministers who were also remanded in custody will be released on bail as an investigation into charges of rebellion, sedition and misuse of public funds continues, it added in a statement.
Supreme Court Judge Pablo Llarena, who had taken on their case late last month, said he believed there was a risk that Junqueras and the three others would repeat their alleged offences.
This, he added, meant there was a "possibility that acts could happen again with serious, immediate and irreparable consequences for the community."
He noted as an example a demonstration in Barcelona in September called when police raided a building in a probe into the upcoming banned referendum.
The protest saw angry demonstrators gather outside the building in the city centre late into the night, trapping police inside for hours.
Independence supporters had hoped that all 10 leaders would be released on Monday just as the official campaign for Catalan elections on December 21st is due to kick off at midnight.
The decision comes as former Catalan president Carles Puigdemont and four other ex-regional ministers face an extradition hearing in Belgium where they fled to after Catalonia declared unilateral independence.