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.
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.
Get the latest election news, live updates and election schedule for Lok Sabha Elections 2019 on ndtv.com/elections. Like us on Facebook or follow us on Twitter and Instagram for updates from each of the 543 parliamentary seats for the 2019 Indian general elections.