An interior ministry body said the blast late Saturday had been set off by munitions on display in the mosque as part of an exhibition commemorating Iran's 1980-1988 war against Iraq.
"The explosion of a bomb or any explosion carried out by opposition elements, be they internal or foreign, is ruled out," the national security council said.
"The blast was caused by some munitions used in a exhibition for the (Iran-Iraq war) martyrs in the mosque," a statement said.
Doubts had been raised in Iran about the authorities' insistence that the blast, which also wounded over 200 people, was not an attack.
The cleric who was leading prayers at the mosque, Mohammad Anjavinejad, said the sheer magnitude of the explosion belied the official version of events.
The reformist Etemad newspaper has also said it was apparent the blast was caused by an attack.
"Giving reasons such as the explosion of a gas capsule or ammunition from an exhibition — when such munitions are neutralised and sealed — show that those who voice these things ignore people's intelligence," it wrote on Monday.
A deadly militant strike of this magnitude would be have been unprecedented in recent years in a stable city like Shiraz, a tourist magnet that does not lie near border zones or have significant ethnic minority populations.
Reports just after the blast described it as a bomb attack but by Sunday local officials said it was an accident and not sabotage.
The interior ministry council indicated that the investigation was still not finished, saying the final results would be announced "in the near future."
One of Iran's most famous cities, Shiraz is popular because of its proximity to important ancient sites from the Achaemenid Empire that ruled much of Asia from 550-331 BC.
