A campaigning Spanish judge dropped plans yesterday to investigate the disappearance of thousands of people during the Civil War and General Franco’s dictatorship after protests from the Roman Catholic Church and right-wing politicians.

Spain’s best-known poet, Federico GarcÍa Lorca, was among the missing whose fate Judge Baltasar Garzon had intended to investigate. Lorca, a left-wing homosexual, was shot by a firing squad with two other men near his home in Granada in 1936. His body is thought to lie in an unmarked grave.

For the first time in Spanish history, the judge attempted to resolve the fate of thousands of left-wingers, union members and other opponents of the regime, who disappeared during the 1936-39 Civil War and 36-year dictatorship.

Judge Garzon ordered exhumations from 25 mass graves containing the bodies of those who were shot by firing squad or murdered on the orders of kangaroo courts.

The judge, who has investigated cases of those who disappeared under dictatorships in Argentina and Chile, launched the controversial action at the request of families of the missing. He alleged that the killings of tens of thousands of civilians were carried out systematically by Franco and his henchmen and accused Franco and 44 leading army officers and members of the Falange – the far-right political party that supported the dictator – of crimes against humanity.

But elements in the conservative opposition Popular Party and the Catholic Church said prosecuting the alleged perpetrators for crimes committed up to 70 years ago would be reopening scars from the past.

The public prosecutor’s office appealed, claiming that the judge would be violating an amnesty agreed by political parties in the spirit of national reconciliation in 1977, two years after Franco’s death. The prosecutor argued that Judge Garzon was “not competent to carry out this investigation” which should be “up to the courts of each region where such atrocities were committed”.

The judge complied with a demand from the public prosecutors that the case should be handled instead by regional courts. Some regions are expected to shelve the investigation.

Judge Garzon, who is best known in Britain for his unsuccessful attempt to arrest the late Chilean dictator General Augusto Pinochet in 1998, started an investigation last month into the disappearance of 114,266 people whose bodies are said to lie in mass graves across Spain.

He maintained that he could investigate because such crimes had no statute of limitations because Spain observed the concept of universal justice.

Earlier this month a panel of judges sitting at the Audiencia Nacional, Spain’s top criminal court, suspended the opening of the mass graves while it examined the public prosecutor’s appeal.

Yesterday Judge Garzon withdrew from the case, but campaigners vowed to continue their fight for justice.

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