The foreign ministry made the statement as countries around the world restrict travel from southern African countries as details of the spread emerged.
Early evidence suggests Omicron has a higher re-infection risk.
The World Health Organization (WHO) said on Friday that the new variant was being considered as "of concern".
Hundreds of passengers arriving in the Netherlands from South Africa are being tested for the new variant.
Some 61 people on two KLM flights tested positive for Covid-19 and have been quarantined at a hotel near Amsterdam's Schiphol airport while they have further tests, Dutch officials said.
The Netherlands is currently struggling with a record-breaking surge in cases. An extended partial lockdown comes into force there on Sunday evening.
The new Omicron variant was first reported to the WHO from South Africa on 24 November.
It has also been identified in Botswana, Belgium, Hong Kong and Israel.
More suspected cases were reported in Germany and the Czech Republic on Saturday.
An official in the German state of Hesse tweeted (in German) that the variant had most probably arrived in the country after "Omicron-typical mutations" were found in someone returning from South Africa.
'Excellent Science'
A statement by the South African foreign ministry on Saturday strongly criticised the travel bans.
"Excellent science should be applauded and not punished," it said.
The bans were "akin to punishing South Africa for its advanced genomic sequencing and the ability to detect new variants quicker".
The statement added that the reaction had been completely different when new variants were discovered elsewhere in the world.
The WHO said the number of cases of this variant, initially named B.1.1.529, appeared to be increasing in almost all of South Africa's provinces.
"This variant has a large number of mutations, some of which are concerning," the UN public health body said in a statement on Friday.
It said "the first known confirmed B.1.1.529 infection was from a specimen collected on 9 November".
The WHO said it would take a few weeks to understand the impact of the new variant, as scientists worked to determine how transmissible it was.
A top UK health official warned that vaccines would "almost certainly" be less effective against the new variant.
But Professor James Naismith, a structural biologist from the University of Oxford, added: "It is bad news but it's not doomsday."
Only about 24% of South Africa's population is fully vaccinated.
US infectious disease chief Dr Anthony Fauci said that while the reports on the new variant threw up a "red flag", it was possible that vaccines might still work to prevent serious illness.
The WHO has warned against countries hastily imposing travel restrictions, saying they should look to a "risk-based and scientific approach".
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