Cardiff’s hopes of flying out of South Africa on Sunday were ended after two positive Covid-19 cases were confirmed in their squad.
The club confirmed one of the cases is suspected to be the Omicron variant that sparked travel restrictions on flights from South Africa to the UK.
A Cardiff statement said: “PCR tests undertaken last night have returned two positive results.”
However, Scarlets have arrived back in Europe.
Cardiff’s Welsh rivals touched down in Dublin at 02:15 GMT, Monday on a flight both teams were scheduled to take.
The Llanelli-based squad then transferred to an “isolation” hotel in Belfast.
The west Wales side’s chairman Simon Muderack told BBC Radio Wales Breakfast all the players and staff had twice tested negative for Covid in the previous 48 hours prior to their departure from South Africa and explained the reasons why they are quarantining in Northern Ireland.
“We did not have access to a quarantine hotel in Wales, so Belfast was the location within the UK that we were able to access that facility,” Muderack told the programme.
“We’ve obviously got 50 people and the system in the UK is under quite a bit of stress now I would imagine with aeroplanes starting to be able to land.
“For us it was quite simply in the limited amount of time that we had where could we find a location that could accommodate our group en-bloc and Belfast was the answer to that and logically with the plane already flying into Dublin geographically it was a relatively convenient solution.”
Irish side Munster also have a positive Covid case and, like Cardiff, must remain in isolation in South Africa.
Cardiff’s playing and coaching staff have “returned to their hotel to isolate”.
Their statement added: “Cardiff Rugby continue to work with the South African Rugby Union, the Welsh Rugby Union and public health authorities both at home and abroad to decide the next course of action.
“The club are also continuing to work with all relevant authorities to secure the travelling party’s return to Wales when safe and appropriate.
“Everybody concerned in this highly challenging situation would like to thank their families, friends, colleagues and the wider rugby family for their many messages of concern and well wishes.
“No further comments will be made at this time.”
South African government guidelines say individuals who test positive for Covid must isolate for 14 days from the day of developing symptoms, not the day of the positive result.
There has been no confirmation that either or both of Cardiff’s cases are symptomatic.
Cardiff were in South Africa to play in the United Rugby Championship, but all the tournament games in the country over this and next weekend have been called off.
In the meantime, Cardiff and Scarlets were attempting to return home as soon as possible.
Cardiff say they were booked onto a charter flight on Sunday afternoon, but their departure has been delayed for an as-yet unspecified duration.
Cardiff’s plight puts a question mark over their ability to host French side Toulouse in the Heineken Champions Cup on Saturday, 11 December.
Current UK rules state anyone arriving from six recently red-listed countries in Africa must isolate in a hotel for 10 days.
South Africa is one of those six nations after the Omicron Covid-19 variant was detected there.