They were among 61 passengers who tested positive for COVID-19 on the two flights, which carried about 600 people. Those who tested positive are being kept in isolation at a hotel near the airport.
"In our (virus) sequencing investigation, which is still ongoing, we have so far found 13 cases of the Omicron variant among the positive (passenger COVID-19) tests," the National Institute for Health (RIVM) said in a statement.
"It is not unlikely more cases will appear in the Netherlands," Health Minister Hugo de Jonge said at a press conference in Rotterdam. "This could possibly be the tip of the iceberg."
The Dutch investigation began with testing of all the people who arrived on the two flights from South Africa at Amsterdam's Schiphol Airport on Friday, before the Dutch government changed its rules on air traffic from southern Africa due to concerns over the variant.
The discovery of Omicron, dubbed a "variant of concern" by the World Health Organization, has sparked worries around the world that it could resist vaccinations and prolong the nearly two-year COVID-19 pandemic.
Dutch health authorities are also seeking to contact and test some 5,000 other passengers who have travelled from South Africa, Botswana, Eswatini, Lesotho, Mozambique, Namibia or Zimbabwe since Monday.
Worries over the variant come as many European countries are already grappling with a surge in coronavirus cases.
In the Netherlands, rules go into effect on Sunday mandating the closure of bars, restaurants and most stores at 5 p.m. in an attempt to reverse a record-breaking wave of COVID-19 cases that is swamping the healthcare system.
(Reporting by Toby Sterling, Bart Meijer, Anthony Deutsch; Editing by Frances Kerry)
By Bart H. Meijer