It was identified in two test samples taken in the country between 19 and 23 November, which is before the variant was first reported by South Africa.
It is not clear whether those who took the tests had visited southern Africa.
It was previously thought that two flights that arrived from South Africa on Sunday had brought the first cases of the variant to the Netherlands.
Fourteen people on the flights to the capital, Amsterdam, tested positive for Omicron, among 61 passengers who were found to have coronavirus.
Early evidence suggests Omicron has a higher re-infection risk. But scientists say it will take about three weeks before it is known how the heavily mutated variant impacts on the effectiveness of vaccines.
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