Update 4.16pm: The EPA said it was told the lime cloud was contained in the building and that the material was not released to the atmosphere.
"The EPA is satisfied that there was no danger to the public or local community from this release," it said.
The agency also said no rubbish was being fed into the incinerator following the incident and no burning has taken place since.
The EPA said Covanta will be compiling a report on the incident, including outlining the necessary corrective and preventative work to avoid a repeat of the incident.
"On foot of this report, and the EPA's own investigation, further action may be considered by the EPA," it warned.
According to Covanta's website, the use of lime is part of "state-of-the-art air pollution control" which states that acid gases from incineration are neutralised using lime.
The incident has sparked an outcry from opponents in Cork where the country's third incinerator is being planned for the harbour.
A decision on whether it should be given the green light has been delayed four times. The latest deferral gave the company behind the project, Indaver, time to address concerns about potential interference with helicopter flights using Haulbowline Naval Base.
Mary O'Leary, spokeswoman with Chase - the Cork Harbour Alliance for A Safe Environment - said: "It is time to put an end to the charade of safety touted by incinerator operators.
"There are hazards involved at every twist and turn in the process as last night's lime cloud incident illustrates."
Ireland has another waste incinerator, the Indaver plant near Duleek, Co Meath which began generating power in 2011.
Update 2.45pm: The general manager of the Poolbeg incinerator’s managing company has said the plant is “absolutely” safe.
His comments came after an accidental leak of lime that left 11 workers in hospital.
Two of them remain in St Vincent's Hospital in Dublin, but are likely to be released this afternoon.
The HSA is carrying out an investigation on site and all testing of the facility has stopped.
Managing Director at Covanta Energy Ireland John Daly said the company is also investigating the cause of the leak, but that people should not be worried.
“We are very good at what we do. We operate 40-off plants in the US and have a very good record there,” he said.
“We will get to the bottom of exactly what the issue is here and make sure it doesn;t happen again.”
In response to a question as to whether the plant is safe, he responded: “Absolutely.”
Update 2.15pm: Green Party leader Eamon Ryan has said the release of lime at the Poolbeg incinerator needs to be fully investigated, and that operations should stop in the interim.
Early investigations suggest the incident late last night was caused by a problem with a door seal, and that a small amount of lime was accidentally released during testing inside the flue gas treatment area.
Eleven men who were removing scaffolding at the time were seen afterwards in hospital, with two remaining in overnight.
Green Party leader Eamon Ryan said the incident needs to be fully investigated. "We've had a concern about this incinerator since the beginning. It should not go into operation until it's found out what is happening here…We have to make sure it's safe," he said.
Dublin City Councillor for the Social Democrats Cian O'Callaghan said the incident was not acceptable, adding: "This is not meant to happen at all."
Update 11am: It has been announced that the 'uncontrolled release' of a substance at Poolbeg incinerator that resulted in 11 workers being taken to hospital concerned a small amount of lime.
The lime was inadvertently released inside the flue during the testing of the new Dublin Waste-to-Energy plant at Ringsend. The plant started burning waste last Thursday after taking its first delivery at the end of April.
The operator Covanta said the lime was contained within the building and did not escape into the environment.
Eleven men were removing scaffolding at the time. They received first aid at the scene after complaining of breathing and vision difficulties.
They attended St Vincent's hosptial as a precaution. Two men were hospitalised overnight.
Health and safety authority inspectors are on site. However, as the area is now closed off, the Environmental Protection Agency has not been able to get its inspectors in.
A spokesperson for for Dublin Waste-to-Energy Ltd said combustion unit No. 1 was shut down in an orderly and controlled manner and the lime did not escape into the environment.
An uncontrolled release has occurred at Poolbeg Incinerator in Dublin.
Eleven men have been treated in hospital following the incident at 6am today.
The HSA says it is treating the incident as a dangerous occurrence. It is not yet known what substance was released.
First aid was administered at the scene and the men attended St Vincent's hospital. Nine men were released, and two are being kept under observation.
HSA and EPA Inspectors due on site and an investigation is underway.