They claimed he had knowingly exceeded his official remit in launching an investigation into tens of thousands of disappearances during Spain's 1936-1939 Civil War and under the Franco regime that followed.
Mr Garzon had ordered the immediate exhumation of civil war-era mass graves.
'Artificial arguments'
In February, Supreme Court investigating magistrate Luciano Varela ruled that Mr Garzon had ignored a 1977 amnesty that covers crimes committed during the civil war.
GARZON'S FAMOUS CASES
Campaigned for extradition of former Chilean military ruler Gen Augusto Pinochet from UK to Spain over human rights abuses in 1998. Request turned down on health grounds
Charged Osama Bin Laden over 9/11 attacks in 2003
Tried unsuccessfully to prosecute Italian politician Silvio Berlusconi on charges of tax fraud and breaching anti-trust laws in Spain through stake in Spanish TV company Telecinco
The amnesty law pardoned politically motivated crimes committed by both sides. By guaranteeing that the past would not be raked over, it underpinned Spain's delicate transition from dictatorship to democracy, correspondents say.
Mr Garzon appealed against the ruling.
But on Wednesday, Mr Varela asserted that Mr Garzon had been aware of his lack of jurisdiction due to the amnesty law.
"Conscious of his lack of jurisdiction... he constructed artificial arguments to justify his control of the penal proceedings," he said in a written ruling.
Gonzalo Martinez-Fresneda, a lawyer for Mr Garzon, said the judge would probably be suspended from his post at the national court in the next few days and that a trial could start as early as June.
Mr Garzon, who is highly popular among the Spanish political left and international human rights campaigners, has strongly denied that he broke the law.
He has been supported by the International Commission of Jurists.
"If this trial goes ahead, it will be the first time that we know of where a judge, who is trying to reach truth, justice and reparation for over 100,000 people who disappeared, is tried," said Esteban Beltran, director of the Spanish branch of Amnesty International.
But some on the right accuse Mr Garzon of launching cases that are politcally motivated.
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