Neruda, a celebrated poet, politician, diplomat and bohemian, died in 1973 aged 69, just days after Pinochet, then the head of the Chilean army, overthrew Socialist president Salvador Allende in a bloody coup.
The writer, who was also a prominent member of the Chilean Communist party, had been preparing to flee into exile in Mexico to lead the resistance against Pinochet's regime.
He died in a Santiago clinic where he was being treated for prostate cancer.
"The (death) certificate does not reflect the real cause of death," Aurelio Luna said at a news conference on behalf of a panel of experts, referring to the official explanation that cancer killed the famed writer.
Doubts emerged in 2011, when his former driver and personal assistant claimed Neruda was given a mysterious injection in his chest just before he died.
Pinochet, who ruled Chile for 17 years, installed a regime that killed some 3,200 leftist activists and other suspected opponents.
He died in 2006 at age 91 without ever being convicted for the crimes committed by his regime.