QAMEA and Matangi Island in Cakaudrove will be declared bio-security or quarantined areas in the first phase of a process to eradicate the iguanas.
The Bio-Security Services Division said the reptile has rapidly increased in numbers and is a threat to islanders' food security.
Division director Ilatia Boa said agriculture minister will make the declaration that is to be gazetted.
"We have already informed the minister and the permanent secretary of the need to make the declaration and will formalise it with a proposal next week," he said.
The declaration will prohibit movement by individuals or groups of the green iguanas from Qamea, Matangi and Laucala Islands to other parts of the Fiji Islands.
Permanent Secretary for Agriculture Colonel Mason Smith confirmed that officers would be sent to the island to set traps for the iguanas once the eradication process gets underway later in the year.
"We decided to eradicate them following the findings of a team that carried out investigations into the reptile last month," he said.
Mr Boa said the findings showed that the reptile, which is a herbivore, devoured vegetables like taro leaves and cabbages.
"The survey was carried out for a week on Taveuni and for two days on Qamea and it was established that the green iguana was first sighted on January 20 this year," he said.
"Three were taken alive and are at Koronivia.
"According to findings, in one birth the iguana lays 60 eggs, so that accounts for the rapidly increasing population," he said. Juveniles were discovered at Yaragau Estate on Qamea - a breeding site.