In a statement issued on Sunday evening, it said work would begin in the early hours of Monday and that Yau Ma Tei Market and Reclamation Street Cooked Food Hawker Bazaar, along with the hawker areas on Reclamation Street and Temple Street, would be deep cleansed and disinfected.
The department said it expected the facilities to reopen at 9 am on Monday.
A spokesman thanked market vendors and hawkers for their cooperation.
The department also said it had been providing refuse collection, street cleaning and public toilet facilities during the lockdown, which began at 4 am on Saturday.