The move came just over a month after MPs passed an amnesty law aimed at drawing a line under years of efforts to prosecute those involved in the botched secession bid that triggered Spain's worst political crisis in decades.
But blocking the amnesty for Puigdemont could complicate life for Spain's Prime Minister Pedro Sanchez, who relied on Catalan parties to secure a new term in office in November.
In a statement, the Supreme Court said judge Pablo Llarena "issued an order declaring the amnesty is not applicable to the crime of misuse of public funds".
It said it agreed to keep in place "the arrest warrants" against him.
Any appeal must be made within three days.
The amnesty law is expected to affect some 400 people, first and foremost Puigdemont, the regional leader at the time of the independence bid who fled Spain to avoid prosecution.
- Disobedience, embezzlement charges -
Sanchez agreed to push through the measure in exchange for the parliamentary support of the Catalan separatist parties that would allow him to serve a new four-year term in office.
After parliament voted to approve the amnesty law on May 30, judges were given two months to apply the law by annulling the charges and cancelling any arrest warrants against the separatists.
But the courts must apply the amnesty on a case-by-case basis, making it a long and drawn-out process.
Last year, the Supreme Court dropped the sedition charges against Puigdemont and two others following a controversial criminal code reform.
Prosecutors filed fresh charges against them for misuse of public funds and disobedience in connection with the independence bid.
In February, the court also opened a "terrorism" probe into Puigdemont over a string of mass street protests by a group called Democratic Tsunami. Spain jailed 13 pro-independence leaders in 2019 over the protests.
In his decision, Llarena said the amnesty law was applicable to the crime of disobedience, but could not be applied in the case of misappropriation of public funds because of two exceptions.
The law allows the amnesty to be applied if the funds were used to finance the pro-independence process, but not if the money was taken for personal gain or if it involved European Union funds.
For that reason, the arrest warrant for Puigdemont would remain in place "for the offence of misuse of public funds but not for disobedience", the judge wrote.
The other case against Puigdemont involving so-called street "terrorism" is being handled separately.
- Court acting as 'vigilante' -
Jordi Turull, secretary general of Puigdemont's hardline separatist JxCat party, said it was "a very serious decision that violates the rule of law" and put the judiciary at odds with the wishes of the state.
"The Supreme Court is bypassing the amnesty law in order to keep acting as a vigilante against the separatists," he wrote on X, describing it as "a clearly political decision".
And Puigdemont himself reacted on X with a three-word post saying: "La Toga Nostra" -- comparing Spain's robe-clad judges to Sicily's Cosa Nostra mafia.
Last month, Llarena informed police that the arrest warrant for Puigdemont would remain in force until a decision were made about whether amnesty could be applied in his case or not.
Many judges have expressed opposition to the amnesty law. Spain's right-wing and far-right opposition has staged months of protests against it, some of which have turned violent.
It has also caused deep rifts within Spanish society and even within Sanchez's own ruling Socialist party.
bur-hmw/bc
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