Spanish MPs in May 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.

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.

The law is expected to affect some 400 people, first and foremost Puigdemont, regional leader at the time of the independence bid, who fled Spain to avoid prosecution.

In a statement, the court said judge Pablo Llarena, who is in charge of the case, "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.

- Disobedience, embezzlement charges -

Sanchez agreed to push through the measure in exchange for the parliamentary support of the Catalan separatist parties for 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 of 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.

- Separate 'terrorism' charge -

The other case against Puigdemont involving so-called street "terrorism" is being handled separately.

Shortly after the announcement, Puigdemont posted a brief message on X, formerly Twitter, referring to "La Toga Nostra" -- comparing the robe-clad judges to Sicily's Costa 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 can 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.

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