Cardiff and Munster are to remain in Cape Town after both clubs returned positive coronavirus tests.
The clubs are among several European rugby union teams that were in South Africa when authorities raised concerns about the new Omicron coronavirus variant.
Munster confirmed one person in their travelling party has tested positive, while Cardiff have returned two positive tests.
They had hoped to join Welsh side Scarlets on a charter flight out of South Africa on Sunday, but will instead stay in their Cape Town hotels. Italian side Zebre are the other team still in the country.
"Munster Rugby will remain in Cape Town while we wait on next steps from the health authorities after returning one positive case in our latest testing," the Irish club said.
"In taking all precautions and prioritising the health and wellbeing of everyone Munster Rugby will not travel today and will return to their hotel for an isolation period as a matter of priority."
Cardiff said: "Cardiff Rugby have been unable to depart South Africa following two positive cases of Covid-19, one of which is suspected to be the new variant Omicron.
"The travelling party had hoped to depart Cape Town this afternoon after a charter plane was secured, however PCR tests undertaken last night have returned two positive results.
"As a consequence of one of these results suspected of being Omicron, the entire travelling party have returned to their hotel to isolate.
"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."
The Munster players will still have to isolate for 10 days on their return to Ireland, which will have a potentially massive impact on their future fixtures.
They are due to play Wasps (December 12) and Castres (December 18) in the European Rugby Champions Cup, fixtures which could now be under threat depending on how long they remain in Cape Town.
Any hotel quarantine in the United Kingdom for Cardiff and Scarlets, which will be the case if rules are applied, will leave them unable to train on the pitch for 10 days and throw preparations for their European Rugby games on December 11 into doubt.
Direct flights from South Africa to Britain were halted on Friday and travellers from southern Africa arriving in Britain and European countries face onerous quarantine restrictions as part of steps to avoid the spread of the Omicron variant of coronavirus detected this week.