Doubts have surrounded the cause of the Nobel laureate's 1973 death since his former driver claimed Neruda was given a mysterious injection in his chest at the Santiago clinic where he was being treated for prostate cancer.
Neruda, who had been planning to leave for Mexico to lead the opposition to Pinochet's regime, died hours after the injection. He was 69.
The cause of death was given as advanced prostate cancer, but in 2011 officials agreed to a request from the Chilean Communist Party, of which Neruda was a member, to exhume his body for analysis.
But a new examination by forensic experts at the Universidad de Murcia in Spain found an unexplainable bacteria, Staphylococcus aureus, in his remains, said judicial officials.
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"It is very difficult to establish or exclude the presence of an acute infectious process in the poet's final hours of life," they said in a statement.
"Analyzing the data requires an ample dose of caution to avoid risky conclusions in the absence of additional information, which we lack at this time."
But Neruda's family said the report fueled their suspicions.
Two other bacteria found in Neruda's body were linked to his cancer, but the Staphylococcus aureus "has no relation with his cancer: that is the news," said Rodrigo Lledo, a lawyer with the Chilean interior ministry's human rights programe.