The Department of Health said the siblings, an 11-year-old boy and 13-year-old girl, are relatives of a Saudi Arabian official in Hong Kong.
The pair had been undergoing self-isolation at home as they are exempted from having to quarantine at a designated quarantine hotel.
The Centre for Health Protection (CHP) said the girl was found to carry the L452R mutant strain.
The other confirmed cases on Wednesday were three women, aged between 27 and 36, who flew in from Bangladesh, Cambodia and the United Arab Emirates.
The CHP said the woman from Bangladesh was also found to be carrying the L452R mutant strain, and test results on the other patients are still pending.
There are fewer than five preliminary positive cases, it added.
Hong Kong has recorded 11,970 confirmed cases since the outbreak of the coronavirus pandemic.