The individual is a non-Malaysian student from South Africa who arrived in the country on November 19, Khairy told a press conference, Xinhua news agency reported.
He said there is no cause for immediate concern as the individual had been quarantined on arrival, with contact tracing being done and exposed individuals being tested.
"The case underwent quarantine alone at the centre and based on the investigation conducted, the student complied with the orders issued. The case is also fully vaccinated and presents no symptoms," he said.
On December 1, the ministry imposed entry restrictions on foreign nationals from eight African countries with a high risk of Omicron infections.
Travellers from Botswana, Eswatini, Lesotho, Mozambique, Namibia, South Africa, Zimbabwe and Malawi will no longer be allowed to enter Malaysia for the time being.
Khairy also said travellers from several countries and regions are temporarily barred from taking part in the Langkawi international travel bubble program, following the detection of cases involving the Omicron variant.
The ban also applies to those with a history of having travelled to these countries and regions within 14 days.
Khairy said the vaccinated travel lane (VTL) between Singapore and Malaysia would continue to operate for the time being.
The Omicron variant was first reported to the World Health Organization (WHO) by South Africa last week. So far, several European countries, as well as countries and regions including Australia, Canada, Israel and China's Hong Kong, have confirmed infections of the variant.
The WHO has called the strain with a large number of mutations a "variant of concern," warning that it may be highly transmissible and pose an increased risk of re-infection to people who have previously been infected with Covid-19.