It was supposed to end the mystery, but the exhumation of Salvador Allende's remains has only fanned confusion and conspiracy theories over how he died, angering relatives who hoped for closure.

Politicians, writers, film-makers and human rights advocates clashed last week over whether Chile's President shot himself or was shot by someone else - or maybe even both - as troops stormed his palace during General Augusto Pinochet's coup on September 11, 1973.

Forensic experts have begun a post-mortem examination to try to determine the truth, but the anguished debate over Allende's death - Latin America's version of the JFK conspiracy - has reopened wounds, doubts and new contradictions.

"We are searching for the truth, but we want that truth to be based on scientific proof, not on journalistic imagination, not on irresponsibility," said Isabel Allende, a senator and daughter of the former President, after a controversial television documentary suggested he was murdered.

Clearly distraught, she called the programme on state channel TVN "an insult to scientific intelligence".

For Chile, it was a week of illustrious ghosts and uneasy questions.

Mario Carroza, the judge investigating the death of Allende and hundreds of others in the coup and its "dirty war" aftermath, added the Nobel prize-winning poet Pablo Neruda to his list. He will examine claims that Pinochet's agents injected poison into Neruda's stomach while he was treated in the Santa Maria clinic in Santiago for prostate cancer, which until now was blamed for his heart failure.

Chile's Communist party demanded the investigation after the poet's former driver, Manuel Araya, said henchmen injected Neruda, 69, with a poison 12 days after the coup. Neruda, a communist and political activist, had just written an article excoriating the new military regime and defending his late friend Allende.

The Neruda Foundation, which administers his estate, has rejected the murder theory and said the author of Twenty Poems of Love and a Song of Despair was gravely ill.

The Allende family seems equally sure the President was not murdered. When medical examiners removed his metallic grey coffin from its mausoleum in Santiago's main cemetery last week the idea was to bring judicial certainty to the belief that the socialist government leader took his own life as Pinochet's soldiers closed in.

To avoid charges of a cover-up, a team of international forensic experts was called in to provide an independent evaluation of the evidence. The final forensic report is expected to be completed in the next 90 days.

Patricio Guijon, one of the President's doctors, had testified that he saw Allende, seated on a sofa, shoot himself under the chin with an AK-47, a gift from the Cuban leader Fidel Castro.

The family came to accept that and depicted it as a courageous act for a man who had loved life.

But even if the post-mortem examination endorses that view, it will be unlikely to silence those who claimed last week that Allende was assassinated by a traitor or shot by a faithful aide in an assisted suicide.

A TV documentary, The Doubt, revealed a 300-page military court report compiled shortly after Pinochet seized power. It said Allende may have been shot in the face with a small firearm before being shot with an assault rifle. A fingerprint analysis of the AK-47 found no prints.

Two forensics experts who analysed the report said they believed he was shot with a small-calibre weapon first. One of them, Luis Ravanal, noted that photographs from the scene showed no signs of blood on Allende's collar, sweater or throat, suggesting someone else fired the AK-47. "The only explanation is that the second bullet was fired when he was already dead and in another position."

The signature at the bottom of the report - Jose Luis Vazquez Fernandez - has set off alarm bells. Vazquez was a doctor notorious for signing what later turned out to be falsified post-mortem reports in the controversial deaths of a child, Rodrigo Anfruns, and Carmelo Soria, a Spanish-Chilean diplomat working with the United Nations.

Vazquez's presence at Allende's original post-mortem has fuelled suspicion of a cover-up by Pinochet's newly formed government.

Castro, among others, has championed the theory of Allende being gunned down, a heroic end in battle concealed by Pinochet. Other allies have rejected the theory because it opens the President's aides to suspicion of killing their boss before the soldiers burst in.

Camilo Taufic, a writer who has investigated the death, is convinced an aide did pull the AK-47's trigger but as an act of mercy after Allende shot himself in the eye in a botched suicide attempt.