Spain's top court acquitted renowned judge Baltasar Garzon on Monday of abuse of power by trying to investigate Franco-era atrocities, in a case that exposed deep wounds dating back to the civil war.

Six members of the seven-strong Supreme Court panel came out in favour of acquitting the 56-year-old, clearing a major obstacle in Garzon's efforts to revive a career which has been stalled by a string of court cases.

Garzon was accused of violating an amnesty by trying to investigate the disappearance of some 114,000 people during the 1936-39 Civil War and General Francisco Franco's dictatorship that ended in 1975.

Garzon had argued that the atrocities were crimes against humanity and not subject to a 1977 amnesty voted through by parliament.

The court ruled that his decision to launch the probe was "a mistake" since there needed to be a suspect still alive, but that the move did not constitute an abuse of power.

"It is not possible in our procedural system to open an inquiry without the final goal of imposing a penalty," the court wrote in its ruling.

Monday's decision came two weeks after the court quashed a bribe-taking case against Garzon, ruling that a three-year statute of limitations had passed.

Garzon had been accused of soliciting sponsorship payments for lectures he gave in New York from five institutions, four of which had been probed in his own courtroom or other courtrooms in the National Court.

However his legal woes are not yet over as Garzon was handed an 11-year supension from the bench earlier this month after he was convicted of illegally ordering wiretaps in a separate corruption case.

Garzon, who came to fame with his efforts to extradite Chile's former dictator Augusto Pinochet from London in 1998, has also taken on Basque militants and even Al-Qaeda.

His supporters argue that the court cases against him were inspired by a desire for revenge by his enemies.

Rights organisations had in particular criticised the decision to pursue Garzon for investigating torture allegations in a trial that exposed the wounds Spain still bears from the Civil War and Franco's ensuing dictatorship.

"The Supreme Court has spared itself further embarrassment by rejecting these ill-advised charges," Reed Brody, a spokesman for the New York-based Human Rights Watch, said.

"Investigating torture and 'disappearances' cannot be considered a crime. But the damage has already been done with the previous conviction of Garzon," the spokesman added.

A group of UN experts including Gabriela Knaul, UN Special Rapporteur on the independence of judges and lawyers, had also voiced concern about the trial.

Although there was no immediate reaction from Garzon to the verdict, he had declared that his conscience was clear when he addresssed the court on the final day of his trial on February 8.

"I took the decisions that I thought were in keeping with the law... to investigate the mass crimes of the disappearance of people," he told the court.

"A judge's duty is to give protection to the victims... who are the main element in this type of crime."

Monday's Supreme Court verdict draws a line under a case which began in May 2010. Garzon was automatically suspended as the judicial inquiry got under way.

The court had agreed to try Garzon in a suit brought against him by two right-wing groups, despite a call from Spain's public prosecutor for the case to be dismissed.

The two-week trial heard testimony from 12 descendants of people killed during the Civil War, who say their relatives lie in mass graves.

One witness, 75-year-old Olga Alcega, told the court how her grandfather was shot dead by Franco's forces in 1936.

"Fear reigned this country. Nobody dared to speak out, it is up to us, the grandchildren of the victims who dare speak," said Alcega, who attended the hearing dressed in black.