Health Secretary Dr James Fong confirmed the cases of interest were Fijian nationals returning from Africa.
"In Fiji, we currently have Covid-positive travellers in quarantine who arrived in the country from African states before we knew about Omicron.
"They have been quarantined in line with the stringent measures we apply to countries we consider a red zone for ongoing viral spread. Their specimens will be forwarded this week overseas for genetic sequencing."
He added that if sequencing, normally conducted in an Australian medical research facility, confirms the presence of omnicron it will spur an escalation of protective measures.
"The Ministry of Health and Medical Services is continuing to improve public health and medical capacities to manage an increase in cases," Dr Fong said
Data shows Omicron was circulating before it was officially identified in southern Africa last week and it has since been detected in more than a dozen countries.
The development comes as international travellers from Australia and the US began flying into Nadi yesterday after Fiji re-opened its border.
Fiji Airways has 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. However, given this new threat our staff will undergo PCR testing as a precautionary measure."
Fiji Airways said the passengers the Ministry of Health were referring to had arrived into the country well before the Omicron threat was discovered.
"We treat this as serious and will tighten our safety procedures," it said.
Until December 1, Fiji's borders were closed to all foreign nationals except for citizens of other countries who had rights to work in the country.
Unwilling to ascertain or confirm the number of currently positivity cases of interest, Dr Fong said genetic sequencing would confirm the variants in Fiji.
Photo file RNZ Pacific Caption: Fiji's Health Secretary Dr James Fong