Capacity at the airport has been reduced to 60 percent after the fire caused the closure of the security gates at terminal three, which handles international flights.
And the situation is showing little sign of improving anytime soon, with a report from the Italian National Institute of Health (ISS) on Friday saying that the full reopening of the terminal will be delayed due to lingering contaminants.
“In order to ensure that air quality standards, in line with the guidelines set by the World Health Organization, are met, we will proceed in a timely manner to ensure the elimination of pollution is complete before [the terminal] is reopened”, the report said.
Passengers have been checking in for flights at other terminals but the increase in traffic is putting a strain on the system, and at the busiest time of the year.
Rachel McNally, who was travelling from Rome to Dubai with Emirates, told The Local that she narrowly made her flight on Sunday due to the confusion and severe delays at security and passport control.
“After discovering that my check-in was actually in terminal one and not three, as my airline told me, the check-in process itself was incredibly confusing because the staff had to explain where my gate was, which involved walking several long corridors and two bus transfers, not to mention the long lines to pass security and passport control.”
Kelly Jenkins, who was also travelling to Dubai, said he felt “panicked” about making his flight, despite giving himself extra time.
"I arrived three hours early," he told The Local.
"But still only made the flight in the nick of time."
Some 11 million passengers passed through Fiumicino airport between January and April, according to official figures, a rise of 8.3 percent on the same period in 2014.
The airport plunged into chaos after the blaze, triggered by an electrical fault, in early May.
It took more than five hours to bring the overnight fire fully under control, by which point it had devastated a shopping area with a string of up-market boutiques.
Staff working near the affected area have been ordered to wear air pollution masks and have seen their shifts cut to a maximum of four hours.
The terminal is one of four at the airport and serves flights to European countries outside the Schengen no-borders zone and destinations further afield with the exception of Israel and the United States.