The government says supplies of vegetables and chilled poultry into Hong Kong may be affected on Sunday, after some mainland goods drivers tested preliminary positive for Covid on Friday.
It said disinfection had been taking place at the border interchange point but some drivers were quarantined.
On Saturday, Shenzhen authorities set up temporary interchange points but the redeployment of drivers will likely have a knock-on effect.
The government said authorities in Hong Kong and Shenzhen were working closely to make sure supplies return to normal.