A Madrid cemetery has been accused of lying about cremating the bodies of 3,000 civilians executed under the brutal regime of Francisco Franco after heavy rains exposed a mass grave.

Recent heavy rain swept away soil in an area of La Almudena public cemetery, exposing the bare bones of people executed on the orders of Francoist military courts in the five years after Spain’s civil war ended in 1939.

The discovery comes as the Spanish government battles to carry out its plan to exhume Franco's body from its gigantic mausoleum, amid protracted legal wranglings.

The new finding contradicts a claim by the municipal funeral company, which said the ossuary containing the remains of those killed during Franco’s post-war repression had been located and the bones cremated in the 1990s.

“It was a genuine surprise, because it had been thought that the ossuary was empty,” said Mauricio Valiente, the head of the city’s Human Rights and Historical Memory department. A survey will be carried out to determine the dimensions of the grave and confirm that the dead are victims of fascist firing squads, he added.