The fire ripped through the warehouse Sunday ahead of a vote recount prompted by allegations of fraud during the election that saw a surprise victory for a populist cleric and Iraqi voters dumping the old guard.
Two hours after the blaze erupted firefighters backed by 10 trucks were still struggling to put out the fire, an AFP reporter said.
Though Interior Minister Qasim al-Araji said no votes were lost, photographs showing the enormous fire and clouds of thick black smoke suggest the warehouse suffered significant damage.
According to Al-Jazeera, Prime Minister's comments were the most high-profile indication that the fire in the Iraqi capital was deliberate."Burning election warehouses ... is a plot to harm the nation and its democracy".
Numerous legislative election losers - including lawmakers and the outgoing PM Haider al-Abadi, whose coalition faltered in the polls by finishing in third place - are claiming foul play behind the fire the engulfed the warehouse.
An interior ministry spokesman told the Reuters news agency that the blaze had destroyed some documents and equipment, but efforts were being made to stop it from affecting ballot boxes.
However, a Baghdad Province council member said that "all the boxes and papers have burned".
Iraqi Parliament Speaker Salim al-Jabouri, meanwhile, claimed the fire was a "planned crime aimed at hiding cases of manipulation and falsification of votes and deceiving the Iraqi people and changing their will and choice".
The fire occurred almost a month after Iraq's parliamentary elections, in which the Sairoon coalition led by Shiite leader Muqtada al-Sadr won 54 seats out of 328.
The extent of the damage caused to ballot boxes was still unclear but some officials have suggested that majority had been spared. Some Iraqi politicians had argued that the manual recount was necessary to make sure that the electronic system did not hide fraud.
Less than half of Iraq's population took part in last month's election in what was widely interpreted as a show of disillusionment with established elites - a trend further demonstrated in the swing to Mr al-Sadr's coalition.
The depot housed ballot boxes from the city's al-Rusafa district.
Abadi's bloc came in third in the election, which was marked by low turnout.
Certain parties are trying to drag Iraq into civil war, he said, adding that he would not participate in one.
The June 11 report said the suspects included three police officers and an employee of Iraq's elections commission.
In an article published by his office, Sadr asked: "Is it not time to stand as one for building and reconstruction, instead of burning ballot boxes or repeating elections just for one seat or two?".
The election marked the first time Iraqi ballots were counted electronically and not by hand.
"Nothing is known, but there are people who would not want the votes to be recounted because it would prove their fraud or they could loose even more votes", federal intelligence officer Abo Musa said.