The pair travelled to Fiji from Nigeria on November 25.
They both tested positive to Covid-19 while in a border quarantine facility.
Health Secretary James Fong said last night their samples were sent to a reference laboratory in Australia for urgent genomic sequencing.
Dr Fong said both travellers' results were confirmed positive for the Omicron variant.
"The two travellers are Fijian citizens who had travelled back into Fiji from Nigeria, arriving on Fiji Airways flight FJ1392 from Hong Kong on November 25th - the day the discovery of the Omicron variant was announced internationally," Dr Fong said.
"Both travellers tested negative for Covid-19 before departure from Fiji and before they left Nigeria.
"They entered a government-designated border quarantine facility immediately upon arrival into Fiji, tested positive while in quarantine, currently have no symptoms, and were fully vaccinated."
With the exception of four passengers, Dr Fong said other passengers on the flight were from non-travel partner countries.
"They had entered a border quarantine facility upon arrival to undergo the full quarantine protocol of 10 days," Dr Fong said.
"That has since been extended to 14 days.
"The four passengers on the flight who were from a travel partner country have tested negative.
"The Fiji Airways crew and accompanying passengers from FJ1392 have tested negative at least twice," Dr Fong said.
Fiji Airways confirmed none of its crew or staff have been given government directives to isolate.
The airline said it had strict protocols which forced all staff to undergo swabs before and after international flights.
"None of our crew are in quarantine or have tested positive to Covid-19. We understand two cases of interest have tested positive but there is no confirmation on which variant it is," Fiji Airways said in a statement.
"However, given this new threat our staff will undergo PCR testing as a precautionary measure."