Authorities at Schipol airport had tested more than 600 passengers from the two flights that had arrived on Friday.
The omicron variant was detected in more than a fifth of the cases, which is feared to be extremely contagious compared to other Covid-19 virus variations.
While experts do not yet know much about it, the variant has been found to have 32 mutations in its spike protein.
Dutch health minister Hugo de Jonge told a press conference in Rotterdam: “It is not unlikely more cases will appear in the Netherlands... this could possibly be the tip of the iceberg.”
The Netherlands is set to go into a new lockdown later on Sunday, which had been planned prior to the discovery of the omicron variant and was due to a surge in the delta variation of the virus.
The Dutch authorities are also attempting to contact 5,000 other passengers who have arrived from South Africa, Botswana, Eswatini, Lesotho, Mozambique, Namibia or Zimbabwe since Monday.
The discovery of omicron, dubbed a “variant of concern” by the World Health Organisation (WHO), has sparked worries that it could resist vaccinations and prolong the pandemic that has gone on for nearly two years.
Omicron was first discovered in southern African nations and has since also been detected in the UK, Germany, Italy, Denmark, Belgium, Botswana, Israel, Australia and Hong Kong.
UK health secretary Sajid Javid has admitted passengers that arrived in the UK from South Africa – before the incoming flights were banned on Friday – were not tested for the variant.
Many countries have banned flights from at least seven nations in southern Africa in attempts to curb the spread of the variant.
Israel has become the first country to shut its borders completely after the discovery of the variant.
The return to travel restrictions has seen financial markets plunge earlier this week over fears that economic recovery will be delayed further.